Fri Mar 14 20:59:01 UTC 2025 I: starting to build salmon/unstable/amd64 on jenkins on '2025-03-14 20:58'
Fri Mar 14 20:59:01 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_5/33799/console.log
Fri Mar 14 20:59:01 UTC 2025 I: Downloading source for unstable/salmon=1.10.2+ds1-1
--2025-03-14 20:59:02-- http://deb.debian.org/debian/pool/main/s/salmon/salmon_1.10.2%2bds1-1.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2558 (2.5K) [text/prs.lines.tag]
Saving to: ‘salmon_1.10.2+ds1-1.dsc’
0K .. 100% 361M=0s
2025-03-14 20:59:02 (361 MB/s) - ‘salmon_1.10.2+ds1-1.dsc’ saved [2558/2558]
Fri Mar 14 20:59:02 UTC 2025 I: salmon_1.10.2+ds1-1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: salmon
Binary: salmon
Architecture: any-amd64 arm64
Version: 1.10.2+ds1-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <crusoe@debian.org>, Kevin Murray <spam@kdmurray.id.au>
Homepage: https://github.com/COMBINE-lab/salmon
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/salmon
Vcs-Git: https://salsa.debian.org/med-team/salmon.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev, libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev (>> 2.0), libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, python3-docs-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev, libsimde-dev
Package-List:
salmon deb science optional arch=any-amd64,arm64
Checksums-Sha1:
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30674e13817eeb27ade3c0ee5073540e9cbda647 1893940 salmon_1.10.2+ds1-1.debian.tar.xz
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6d296a4cb41e4068975b0ff8592d700cd525a2f961c7fc10ba54cdc69cfe2456 1893940 salmon_1.10.2+ds1-1.debian.tar.xz
Files:
142f7da8a6cde566343ae6f3431d7a39 5718424 salmon_1.10.2+ds1.orig.tar.xz
07a9180c1b0c41c4dae2adb41ac2e605 1893940 salmon_1.10.2+ds1-1.debian.tar.xz
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Fri Mar 14 20:59:02 UTC 2025 I: Checking whether the package is not for us
Fri Mar 14 20:59:02 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net.
Fri Mar 14 20:59:02 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net.
Fri Mar 14 21:19:16 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Fri Mar 14 08:59:11 -12 2025
I: pbuilder-time-stamp: 1741985951
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [salmon_1.10.2+ds1-1.dsc]
I: copying [./salmon_1.10.2+ds1.orig.tar.xz]
I: copying [./salmon_1.10.2+ds1-1.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./salmon_1.10.2+ds1-1.dsc: unsupported subcommand
dpkg-source: info: extracting salmon in salmon-1.10.2+ds1
dpkg-source: info: unpacking salmon_1.10.2+ds1.orig.tar.xz
dpkg-source: info: unpacking salmon_1.10.2+ds1-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying spelling
dpkg-source: info: applying use_debian_packaged_libs.patch
dpkg-source: info: applying pufferfish
dpkg-source: info: applying disable-version-check.patch
dpkg-source: info: applying sphinx.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1830931/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='c8ee5e80bec34930a2482241e18c8f66'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='1830931'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.LV3asmU0/pbuilderrc_nw6y --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.LV3asmU0/b1 --logfile b1/build.log salmon_1.10.2+ds1-1.dsc'
SUDO_GID='111'
SUDO_UID='106'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://46.16.76.132:3128'
I: uname -a
Linux ionos11-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1830931/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev, libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev (>> 2.0), libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, python3-docs-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev, libsimde-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19785 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on cmake; however:
Package cmake is not installed.
pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however:
Package libboost-filesystem-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-system-dev; however:
Package libboost-system-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however:
Package libboost-iostreams-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-thread-dev; however:
Package libboost-thread-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however:
Package libboost-program-options-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-timer-dev; however:
Package libboost-timer-dev is not installed.
pbuilder-satisfydepends-dummy depends on libjellyfish-2.0-dev; however:
Package libjellyfish-2.0-dev is not installed.
pbuilder-satisfydepends-dummy depends on libpthread-stubs0-dev; however:
Package libpthread-stubs0-dev is not installed.
pbuilder-satisfydepends-dummy depends on libsparsehash-dev; however:
Package libsparsehash-dev is not installed.
pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however:
Package libdivsufsort-dev is not installed.
pbuilder-satisfydepends-dummy depends on libbwa-dev; however:
Package libbwa-dev is not installed.
pbuilder-satisfydepends-dummy depends on pkg-config; however:
Package pkg-config is not installed.
pbuilder-satisfydepends-dummy depends on libjemalloc-dev; however:
Package libjemalloc-dev is not installed.
pbuilder-satisfydepends-dummy depends on libcereal-dev; however:
Package libcereal-dev is not installed.
pbuilder-satisfydepends-dummy depends on libtbb-dev; however:
Package libtbb-dev is not installed.
pbuilder-satisfydepends-dummy depends on libgff-dev (>> 2.0); however:
Package libgff-dev is not installed.
pbuilder-satisfydepends-dummy depends on libstaden-read-dev; however:
Package libstaden-read-dev is not installed.
pbuilder-satisfydepends-dummy depends on libspdlog-dev; however:
Package libspdlog-dev is not installed.
pbuilder-satisfydepends-dummy depends on libtclap-dev; however:
Package libtclap-dev is not installed.
pbuilder-satisfydepends-dummy depends on help2man; however:
Package help2man is not installed.
pbuilder-satisfydepends-dummy depends on sphinx-doc; however:
Package sphinx-doc is not installed.
pbuilder-satisfydepends-dummy depends on python3-sphinx; however:
Package python3-sphinx is not installed.
pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however:
Package python3-sphinx-rtd-theme is not installed.
pbuilder-satisfydepends-dummy depends on python3-docs-theme; however:
Package python3-docs-theme is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libeigen3-dev; however:
Package libeigen3-dev is not installed.
pbuilder-satisfydepends-dummy depends on libbz2-dev; however:
Package libbz2-dev is not installed.
pbuilder-satisfydepends-dummy depends on liblzma-dev; however:
Package liblzma-dev is not installed.
pbuilder-satisfydepends-dummy depends on rapmap-dev; however:
Package rapmap-dev is not installed.
pbuilder-satisfydepends-dummy depends on libsimde-dev; however:
Package libsimde-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} cmake{a} cmake-data{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docutils-common{a} docutils-doc{a} dwz{a} file{a} fonts-font-awesome{a} fonts-lato{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} icu-devtools{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost-timer-dev{a} libboost-timer1.83-dev{a} libboost-timer1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbwa-dev{a} libbz2-dev{a} libcares2{a} libcereal-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdivsufsort-dev{a} libdivsufsort3{a} libeigen3-dev{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfmt-dev{a} libfmt10{a} libgff-dev{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhtscodecs-dev{a} libhtscodecs2{a} libhwloc15{a} libicu-dev{a} libicu76{a} libidn2-0{a} libidn2-dev{a} libjellyfish-2.0-2{a} libjellyfish-2.0-dev{a} libjemalloc-dev{a} libjemalloc2{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblocale-gettext-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libnode115{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpthread-stubs0-dev{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsimde-dev{a} libsparsehash-dev{a} libspdlog-dev{a} libspdlog1.15{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libstaden-read-dev{a} libstaden-read14t64{a} libtasn1-6{a} libtasn1-6-dev{a} libtbb-dev{a} libtbb12{a} libtbbbind-2-5{a} libtbbmalloc2{a} libtclap-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} node-acorn{a} node-balanced-match{a} node-brace-expansion{a} node-cjs-module-lexer{a} node-commander{a} node-corepack{a} node-mathjax-full{a} node-minimatch{a} node-mj-context-menu{a} node-speech-rule-engine{a} node-undici{a} node-xtend{a} nodejs{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python-babel-localedata{a} python-requests-doc{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-doc{a} python3-docs-theme{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-urllib3{a} python3.13{a} python3.13-doc{a} python3.13-minimal{a} rapidjson-dev{a} rapmap-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-doc{a} sphinx-rtd-theme-common{a} tzdata{a} xml-core{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
bzip2-doc curl javascript-common krb5-locales libarchive-cpio-perl libhwloc-plugins libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx nodejs-doc psmisc publicsuffix python3-pil wget
0 packages upgraded, 228 newly installed, 0 to remove and 0 not upgraded.
Need to get 154 MB of archives. After unpacking 819 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 fonts-lato all 2.015-1 [2780 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-2 [859 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-2 [2210 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [1952 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-2 [746 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.2-2 [28.1 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.1-1 [1427 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-2 [337 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-2 [109 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-2 [43.5 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-7 [294 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.6-1 [2268 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-3 [9721 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.3+b1 [699 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-1 [109 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB]
Get: 52 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-2 [194 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB]
Get: 55 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB]
Get: 62 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB]
Get: 64 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.6-1 [12.0 MB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 68 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 71 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 73 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 76 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 docutils-doc all 0.21.2+dfsg-2 [1122 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 76.1-3 [215 kB]
Get: 85 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-5 [60.0 kB]
Get: 86 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-5 [42.5 kB]
Get: 87 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-5 [42.6 kB]
Get: 88 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-5 [54.2 kB]
Get: 89 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-5 [126 kB]
Get: 90 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4.1+b2 [10.6 MB]
Get: 91 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83.0 amd64 1.83.0-4.1+b2 [234 kB]
Get: 92 http://deb.debian.org/debian unstable/main amd64 libboost-atomic1.83-dev amd64 1.83.0-4.1+b2 [236 kB]
Get: 93 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-4.1+b2 [240 kB]
Get: 94 http://deb.debian.org/debian unstable/main amd64 libboost-chrono1.83-dev amd64 1.83.0-4.1+b2 [246 kB]
Get: 95 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83.0 amd64 1.83.0-4.1+b2 [230 kB]
Get: 96 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-4.1+b2 [334 kB]
Get: 97 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-4.1+b2 [373 kB]
Get: 98 http://deb.debian.org/debian unstable/main amd64 libboost-date-time1.83-dev amd64 1.83.0-4.1+b2 [240 kB]
Get: 99 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-4.1+b2 [282 kB]
Get: 100 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83.0 amd64 1.83.0-4.1+b2 [231 kB]
Get: 101 http://deb.debian.org/debian unstable/main amd64 libboost-system1.83-dev amd64 1.83.0-4.1+b2 [232 kB]
Get: 102 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-4.1+b2 [298 kB]
Get: 103 http://deb.debian.org/debian unstable/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B]
Get: 104 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-4.1+b2 [330 kB]
Get: 105 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 76.1-3 [10.8 MB]
Get: 106 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-4.1+b2 [346 kB]
Get: 107 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-4.1+b2 [261 kB]
Get: 108 http://deb.debian.org/debian unstable/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B]
Get: 109 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.1+b2 [347 kB]
Get: 110 http://deb.debian.org/debian unstable/main amd64 libboost-program-options1.83-dev amd64 1.83.0-4.1+b2 [376 kB]
Get: 111 http://deb.debian.org/debian unstable/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B]
Get: 112 http://deb.debian.org/debian unstable/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B]
Get: 113 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83.0 amd64 1.83.0-4.1+b2 [269 kB]
Get: 114 http://deb.debian.org/debian unstable/main amd64 libboost-thread1.83-dev amd64 1.83.0-4.1+b2 [277 kB]
Get: 115 http://deb.debian.org/debian unstable/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B]
Get: 116 http://deb.debian.org/debian unstable/main amd64 libboost-timer1.83.0 amd64 1.83.0-4.1+b2 [235 kB]
Get: 117 http://deb.debian.org/debian unstable/main amd64 libboost-timer1.83-dev amd64 1.83.0-4.1+b2 [237 kB]
Get: 118 http://deb.debian.org/debian unstable/main amd64 libboost-timer-dev amd64 1.83.0.2+b2 [3716 B]
Get: 119 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB]
Get: 120 http://deb.debian.org/debian unstable/main amd64 libbwa-dev amd64 0.7.18-1 [156 kB]
Get: 121 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB]
Get: 122 http://deb.debian.org/debian unstable/main amd64 libcares2 amd64 1.34.4-2.1 [97.9 kB]
Get: 123 http://deb.debian.org/debian unstable/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB]
Get: 124 http://deb.debian.org/debian unstable/main amd64 libcereal-dev amd64 1.3.2+dfsg-5 [221 kB]
Get: 125 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB]
Get: 126 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB]
Get: 127 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB]
Get: 128 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB]
Get: 129 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB]
Get: 130 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB]
Get: 131 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB]
Get: 132 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.8-1 [102 kB]
Get: 133 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB]
Get: 134 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB]
Get: 135 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB]
Get: 136 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB]
Get: 137 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB]
Get: 138 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB]
Get: 139 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-5 [16.1 kB]
Get: 140 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.9+dfsg-2 [311 kB]
Get: 141 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB]
Get: 142 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB]
Get: 143 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB]
Get: 144 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB]
Get: 145 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB]
Get: 146 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB]
Get: 147 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB]
Get: 148 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB]
Get: 149 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 150 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB]
Get: 151 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB]
Get: 152 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB]
Get: 153 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB]
Get: 154 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.12.1-3 [480 kB]
Get: 155 http://deb.debian.org/debian unstable/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB]
Get: 156 http://deb.debian.org/debian unstable/main amd64 libdivsufsort-dev amd64 2.0.1-6+b1 [19.1 kB]
Get: 157 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB]
Get: 158 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB]
Get: 159 http://deb.debian.org/debian unstable/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB]
Get: 160 http://deb.debian.org/debian unstable/main amd64 libfmt-dev amd64 10.1.1+ds1-4 [177 kB]
Get: 161 http://deb.debian.org/debian unstable/main amd64 libgff-dev amd64 2.0.0-3 [154 kB]
Get: 162 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB]
Get: 163 http://deb.debian.org/debian unstable/main amd64 libhtscodecs-dev amd64 1.6.1-2 [3000 kB]
Get: 164 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.12.0-1 [164 kB]
Get: 165 http://deb.debian.org/debian unstable/main amd64 libjellyfish-2.0-2 amd64 2.3.1-4+b1 [67.3 kB]
Get: 166 http://deb.debian.org/debian unstable/main amd64 libjellyfish-2.0-dev amd64 2.3.1-4+b1 [138 kB]
Get: 167 http://deb.debian.org/debian unstable/main amd64 libjemalloc2 amd64 5.3.0-3 [274 kB]
Get: 168 http://deb.debian.org/debian unstable/main amd64 libjemalloc-dev amd64 5.3.0-3 [490 kB]
Get: 169 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 170 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 171 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB]
Get: 172 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB]
Get: 173 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.4-1 [323 kB]
Get: 174 http://deb.debian.org/debian unstable/main amd64 node-xtend all 4.0.2-3 [3932 B]
Get: 175 http://deb.debian.org/debian unstable/main amd64 node-corepack all 0.24.0-4 [704 kB]
Get: 176 http://deb.debian.org/debian unstable/main amd64 nodejs amd64 20.19.0+dfsg-1 [350 kB]
Get: 177 http://deb.debian.org/debian unstable/main amd64 node-acorn all 8.8.1+ds+~cs25.17.7-2 [128 kB]
Get: 178 http://deb.debian.org/debian unstable/main amd64 node-cjs-module-lexer all 1.2.3+dfsg-1 [30.6 kB]
Get: 179 http://deb.debian.org/debian unstable/main amd64 node-balanced-match all 2.0.0-1 [4872 B]
Get: 180 http://deb.debian.org/debian unstable/main amd64 node-brace-expansion all 2.0.1+~1.1.0-1 [7912 B]
Get: 181 http://deb.debian.org/debian unstable/main amd64 node-minimatch all 9.0.3-5 [76.7 kB]
Get: 182 http://deb.debian.org/debian unstable/main amd64 node-undici all 7.3.0+dfsg1+~cs24.12.11-1 [333 kB]
Get: 183 http://deb.debian.org/debian unstable/main amd64 libnode115 amd64 20.19.0+dfsg-1 [12.1 MB]
Get: 184 http://deb.debian.org/debian unstable/main amd64 libpthread-stubs0-dev amd64 0.5-1 [5168 B]
Get: 185 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-3 [467 kB]
Get: 186 http://deb.debian.org/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB]
Get: 187 http://deb.debian.org/debian unstable/main amd64 libspdlog1.15 amd64 1:1.15.1+ds-1 [108 kB]
Get: 188 http://deb.debian.org/debian unstable/main amd64 libspdlog-dev amd64 1:1.15.1+ds-1 [90.8 kB]
Get: 189 http://deb.debian.org/debian unstable/main amd64 libstaden-read14t64 amd64 1.15.0-1.1+b2 [268 kB]
Get: 190 http://deb.debian.org/debian unstable/main amd64 libstaden-read-dev amd64 1.15.0-1.1+b2 [347 kB]
Get: 191 http://deb.debian.org/debian unstable/main amd64 libtbbbind-2-5 amd64 2022.0.0-2 [14.6 kB]
Get: 192 http://deb.debian.org/debian unstable/main amd64 libtbbmalloc2 amd64 2022.0.0-2 [49.3 kB]
Get: 193 http://deb.debian.org/debian unstable/main amd64 libtbb12 amd64 2022.0.0-2 [91.0 kB]
Get: 194 http://deb.debian.org/debian unstable/main amd64 libtbb-dev amd64 2022.0.0-2 [199 kB]
Get: 195 http://deb.debian.org/debian unstable/main amd64 libtclap-dev amd64 1.2.5-1+b2 [3359 kB]
Get: 196 http://deb.debian.org/debian unstable/main amd64 node-commander all 9.4.1-1 [65.3 kB]
Get: 197 http://deb.debian.org/debian unstable/main amd64 node-mj-context-menu all 0.9.1+ds-2 [69.9 kB]
Get: 198 http://deb.debian.org/debian unstable/main amd64 node-speech-rule-engine all 4.0.7+~0.1.31-2 [532 kB]
Get: 199 http://deb.debian.org/debian unstable/main amd64 node-mathjax-full all 3.2.2+~cs4.2.1-4 [3660 kB]
Get: 200 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB]
Get: 201 http://deb.debian.org/debian unstable/main amd64 python-requests-doc all 2.32.3+dfsg-4 [196 kB]
Get: 202 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get: 203 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.17.0-1 [117 kB]
Get: 204 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B]
Get: 205 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 206 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB]
Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB]
Get: 208 http://deb.debian.org/debian unstable/main amd64 python3.13-doc all 3.13.2-2 [15.3 MB]
Get: 209 http://deb.debian.org/debian unstable/main amd64 python3-doc all 3.13.2-2 [10.3 kB]
Get: 210 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.1.3-5 [617 kB]
Get: 211 http://deb.debian.org/debian unstable/main amd64 python3-roman all 5.0-1 [10.6 kB]
Get: 212 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B]
Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB]
Get: 215 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.5-2 [107 kB]
Get: 216 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB]
Get: 217 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB]
Get: 218 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.10-1 [42.0 kB]
Get: 219 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.3.0-2 [114 kB]
Get: 220 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB]
Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.1.3-5 [468 kB]
Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-docs-theme all 2025.2-1 [19.4 kB]
Get: 224 http://deb.debian.org/debian unstable/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB]
Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B]
Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB]
Get: 227 http://deb.debian.org/debian unstable/main amd64 rapmap-dev all 0.15.0+dfsg-4 [193 kB]
Get: 228 http://deb.debian.org/debian unstable/main amd64 sphinx-doc all 8.1.3-5 [3487 kB]
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done.
Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/salmon-1.10.2+ds1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../salmon_1.10.2+ds1-1_source.changes
dpkg-buildpackage: info: source package salmon
dpkg-buildpackage: info: source version 1.10.2+ds1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean --with sphinxdoc
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1'
dh_auto_clean
rm -rf external
rm -f debian/*.1
rm -Rf sample_data
cd doc && /usr/bin/make clean
make[2]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/doc'
rm -rf build/*
make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/doc'
rm -rf tests/unitTests
make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1'
dh_clean
debian/rules binary
dh binary --with sphinxdoc
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1'
# See here
# https://github.com/COMBINE-lab/salmon/issues/87
# for a discussion with upstream why it is necessary to include rapmap source
mkdir -p /build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap
cp -av /usr/share/rapmap/src/* /build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap
'/usr/share/rapmap/src/HitManager.cpp' -> '/build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap/HitManager.cpp'
'/usr/share/rapmap/src/RapMapFileSystem.cpp' -> '/build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap/RapMapFileSystem.cpp'
'/usr/share/rapmap/src/RapMapSAIndex.cpp' -> '/build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap/RapMapSAIndex.cpp'
'/usr/share/rapmap/src/RapMapSAIndexer.cpp' -> '/build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap/RapMapSAIndexer.cpp'
'/usr/share/rapmap/src/RapMapUtils.cpp' -> '/build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap/RapMapUtils.cpp'
'/usr/share/rapmap/src/bit_array.c' -> '/build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap/bit_array.c'
'/usr/share/rapmap/src/rank9b.cpp' -> '/build/reproducible-path/salmon-1.10.2+ds1/external/install/src/rapmap/rank9b.cpp'
dh_auto_configure -- -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE
cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE ..
CC: gcc
CC version:
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
Detected non-ARM host. Setting USE_ARM to false.
version: 1.10.2
-- CMAKE_BUILD_TYPE = Release
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
Building with CONDA_BUILD flag
Making Release build
setting -DHAVE_NUMERIC_LIMITS128
CMake Warning (dev) at CMakeLists.txt:314 (exec_program):
Policy CMP0153 is not set: The exec_program command should not be called.
Run "cmake --help-policy CMP0153" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
Use execute_process() instead.
This warning is for project developers. Use -Wno-dev to suppress it.
running cd "/build/reproducible-path/salmon-1.10.2+ds1" && cp -r ./debian/external ./ 2>&1
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1")
-- Performing Test Iconv_IS_BUILT_IN
-- Performing Test Iconv_IS_BUILT_IN - Success
-- Found Iconv: built in to C library
-- Found LibLZMA: lzma (found version "5.6.4")
Found liblzma library: lzma
===========================================
-- Found BZip2: -lbz2 (found version "1.0.8")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
Found libbz2 library: -lbz2
===========================================
CMake Warning (dev) at CMakeLists.txt:429 (find_package):
Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake
--help-policy CMP0167" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.59.0") found components: iostreams system filesystem timer chrono program_options
BOOST_INCLUDEDIR =
BOOST_LIBRARYDIR =
Boost_FOUND = TRUE
BOOST ROOT =
BOOST INCLUDE DIR = /usr/include
BOOST INCLUDE DIRS = /usr/include
BOOST LIB DIR = /usr/lib/x86_64-linux-gnu
BOOST LIBRARIES = Boost::iostreams;Boost::system;Boost::filesystem;Boost::timer;Boost::chrono;Boost::program_options
-- Found cereal: /usr/include (found suitable version "1.3.2", minimum required is "1.3.2")
-- cereal found (include: /usr/include)
FOUND SUITABLE TBB VERSION : 2022.0.0
-- libgff ver. 2.0.0 found.
-- include: /usr/include/
-- lib : /usr/lib/
-- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "8.12.1")
-- Found libstadenio: /usr/lib/x86_64-linux-gnu/libstaden-read.so (Required is at least version "1.14.15")
-- Staden IOLib found (include: /usr/include)
-- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1")
-- Found Jemalloc: /usr/lib/x86_64-linux-gnu/libjemalloc.so (found version "5.3.0-0-g54eaed1d8b56b1aa528be3bdd1877e59c56fa90c")
Found Jemalloc library --- using this memory allocator
CPACK_SOURCE_IGNORE_FILES = /src/PCA.cpp;/src/PCAUtils.cpp;/build/;/scripts/AggregateToGeneLevel.py;/scripts/ExpressionTools.py;/scripts/GenerateExpressionFiles.sh;/scripts/ParseSoftFile.py;/scripts/PlotCorrelation.py;/scripts/junk;/scripts/sfstrace.log;/scripts/SFPipeline.py;/bin/;/lib/;/sample_data/;PublishREADMEToWebsite.sh;/external/;/src/obsolete/;/include/obsolete/;WebsiteHeader.txt;/experimental_configs/;.git/
CC: /usr/bin/cc
CC version:
version: 1.0.0
Building basic pufferfish components for salmon
setting -DHAVE_NUMERIC_LIMITS128
CMake Deprecation Warning at external/pufferfish/external/ntcard/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
CMake Deprecation Warning at external/pufferfish/external/twopaco/graphdump/CMakeLists.txt:2 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- setting COMPACT_VECTOR_DIR for graphdump to be /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump
CMake Deprecation Warning at external/pufferfish/external/twopaco/graphconstructor/CMakeLists.txt:2 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
add library puffer : PufferfishIndexer.cpp;PufferfishBaseIndex.cpp;PufferfishIndex.cpp;PufferfishSparseIndex.cpp;PufferfishLossyIndex.cpp;edlib.cpp;Util.cpp;rank9sel.cpp;rank9b.cpp;PufferfishValidate.cpp;PufferfishStats.cpp;PufferfishTestLookup.cpp;PufferfishExamine.cpp;PufferfishKmerQuery.cpp;FastxParser.cpp;PufferfishBinaryGFAReader.cpp;PufferFS.cpp;xxhash.c;FixFasta.cpp;MemCollector.cpp;MemChainer.cpp;PuffAligner.cpp;PufferfishAligner.cpp;RefSeqConstructor.cpp;metro/metrohash64.cpp;/build/reproducible-path/salmon-1.10.2+ds1/src/LibraryFormat.cpp
adding /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump to include path for libpuffer
fetched path for compact_vector as [/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump]
NO_IPO = FALSE
TBB_LIBRARIES =
TBB_LIB_INSTALL_DIR =
TBBGLOBS =
-- Configuring done (14.9s)
-- Generating done (0.1s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
FETCHCONTENT_FULLY_DISCONNECTED
FETCHED_RAPMAP
-- Build files have been written to: /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu
make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1'
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1'
dh_auto_build
cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1
make[2]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/salmon-1.10.2+ds1 -B/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
make -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend
make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
make -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/DependInfo.cmake "--color="
make -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend
make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/DependInfo.cmake "--color="
make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend
make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake "--color="
make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend
make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake "--color="
make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/depend
make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake "--color="
make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend
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cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
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cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -MF CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o.d -o CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common/SignalHandler.cpp
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cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -MF CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o.d -o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common/Fcontrol.cpp
make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
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make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/build
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o -MF CMakeFiles/ntcard.dir/nthll.cpp.o.d -o CMakeFiles/ntcard.dir/nthll.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/nthll.cpp
[ 4%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -MF CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/dnachar.cpp
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make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[ 6%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o -MF CMakeFiles/graphdump.dir/graphdump.cpp.o.d -o CMakeFiles/graphdump.dir/graphdump.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/graphdump.cpp
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o -MF CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o.d -o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/dnachar.cpp
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cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o.d -o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp
[ 8%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extd.c
[ 9%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o
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[ 12%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o
[ 12%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o
[ 13%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o -MF CMakeFiles/twopaco.dir/constructor.cpp.o.d -o CMakeFiles/twopaco.dir/constructor.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c
[ 15%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o
[ 16%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c
[ 16%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/kalloc.c
[ 17%] Building CXX object src/CMakeFiles/alevin_core.dir/edlib.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -MF CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o.d -o CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/jellyfish/mer_dna.cc
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/edlib.cpp.o -MF CMakeFiles/alevin_core.dir/edlib.cpp.o.d -o CMakeFiles/alevin_core.dir/edlib.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/edlib.cpp
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -MF CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o.d -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o -MF CMakeFiles/twopaco.dir/compressedstring.cpp.o.d -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp
[ 18%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndexer.cpp
[ 19%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c
[ 20%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extz.c
make -f src/CMakeFiles/UnitTestsMain.dir/build.make src/CMakeFiles/UnitTestsMain.dir/depend
[ 21%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o
make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/UnitTestsMain.dir/DependInfo.cmake "--color="
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp
make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
make -f src/CMakeFiles/UnitTestsMain.dir/build.make src/CMakeFiles/UnitTestsMain.dir/build
make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[ 21%] Building CXX object src/CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -MF CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o.d -o CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/tests/UnitTests.cpp
[ 22%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_gg.c
[ 22%] Building CXX object src/CMakeFiles/salmon_core.dir/backtrace.cc.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/backtrace.cc.o -MF CMakeFiles/salmon_core.dir/backtrace.cc.o.d -o CMakeFiles/salmon_core.dir/backtrace.cc.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/backtrace.cc
[ 23%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2.c
[ 24%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o -MF CMakeFiles/twopaco.dir/test.cpp.o.d -o CMakeFiles/twopaco.dir/test.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp
[ 24%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2_sse.c
[ 24%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -MF CMakeFiles/twopaco.dir/vertexenumerator.cpp.o.d -o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp
[ 25%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp
[ 26%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/xxhash.c.o -MF CMakeFiles/salmon_core.dir/xxhash.c.o.d -o CMakeFiles/salmon_core.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/xxhash.c
cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C
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[ 27%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -MF CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o.d -o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SingleCellProtocols.cpp
[ 28%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -MF CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o.d -o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/TranscriptGroup.cpp
[ 29%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -MF CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o.d -o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp
[ 30%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -MF CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp
make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[ 31%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o
[ 31%] Built target ksw2pp_sse4
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -MF CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o.d -o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/EffectiveLengthStats.cpp
[ 32%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -MF CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o.d -o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/LibraryFormat.cpp
[ 33%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -MF CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o.d -o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/GenomicFeature.cpp
[ 34%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -MF CMakeFiles/salmon_core.dir/VersionChecker.cpp.o.d -o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/VersionChecker.cpp
make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[ 34%] Built target ksw2pp_sse2
[ 35%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp
[ 36%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndex.cpp
[ 37%] Linking CXX static library libntcard.a
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -E cmake_link_script CMakeFiles/ntcard.dir/link.txt --verbose=1
/usr/bin/ar qc libntcard.a CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o CMakeFiles/ntcard.dir/nthll.cpp.o
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make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[ 38%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o -MF CMakeFiles/twopaco.dir/common.cpp.o.d -o CMakeFiles/twopaco.dir/common.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/common.cpp
[ 38%] Built target ntcard
[ 39%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp
[ 39%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishLossyIndex.cpp
[ 40%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SBModel.cpp.o -MF CMakeFiles/salmon_core.dir/SBModel.cpp.o.d -o CMakeFiles/salmon_core.dir/SBModel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SBModel.cpp
[ 40%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o -MF CMakeFiles/salmon_core.dir/FastxParser.cpp.o.d -o CMakeFiles/salmon_core.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[ 40%] Built target ksw2pp_basic
[ 41%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o -MF CMakeFiles/puffer.dir/edlib.cpp.o.d -o CMakeFiles/puffer.dir/edlib.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/edlib.cpp
make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend
make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/build
make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[ 42%] Linking CXX static library libksw2pp.a
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1
"/usr/bin/gcc-ar-14" qc libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o
"/usr/bin/gcc-ranlib-14" libksw2pp.a
make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[ 42%] Built target ksw2pp
[ 43%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinOpts.hpp:5,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SingleCellProtocols.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/src/SingleCellProtocols.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o -MF CMakeFiles/puffer.dir/Util.cpp.o.d -o CMakeFiles/puffer.dir/Util.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/Util.cpp
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishIndex.hpp:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndex.cpp:9:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBaseIndex.hpp:14,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishLossyIndex.hpp:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishLossyIndex.cpp:7:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 44%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -MF CMakeFiles/salmon_core.dir/StadenUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/StadenUtils.cpp
[ 45%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o -MF CMakeFiles/puffer.dir/rank9sel.cpp.o.d -o CMakeFiles/puffer.dir/rank9sel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/rank9sel.cpp
[ 46%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonUtils.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishSparseIndex.hpp:13,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp:10:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/Util.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 47%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o -MF CMakeFiles/puffer.dir/rank9b.cpp.o.d -o CMakeFiles/puffer.dir/rank9b.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/rank9b.cpp
[ 48%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -MF CMakeFiles/puffer.dir/PufferfishValidate.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishValidate.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:27,
from /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 49%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -MF CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/DistributionUtils.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_mk_destructive_iterator(dest_it) const [with Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >*, std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >; dest_it = spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >*, std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_begin() [with Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >*, std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >]'
2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); }
| ^~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_move_from(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = long unsigned int]'
2817 | for (destructive_iterator it = ht.destructive_begin();
| ~~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = long unsigned int]'
2948 | _move_from(mover, ht, min_buckets_wanted);
| ^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_resize_delta(size_type) [with Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = long unsigned int]'
2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
| ^~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; value_type = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >]'
3278 | if (_resize_delta(1))
| ^~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector<std::pair<long unsigned int, bool> >; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; mapped_type = std::vector<std::pair<long unsigned int, bool> >]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here
161 | path[ref_cnt].resize(contigCntPerPath);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >*, std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >*, std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >&)' is deprecated [-Wdeprecated-copy]
2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; }
| ^~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >*, std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >' has user-provided 'spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>& spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>::operator=(const spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>&) [with T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; row_it = spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >*; col_it = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >]'
946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
| ^~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; value_type = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; reference = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; pointer = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; reference = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; reference = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; value_type = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector<std::pair<long unsigned int, bool> >; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; mapped_type = std::vector<std::pair<long unsigned int, bool> >]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here
161 | path[ref_cnt].resize(contigCntPerPath);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >::value_type' {aka 'std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >'} to 'spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >::mutable_reference' {aka 'std::pair<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector<std::pair<long unsigned int, bool> >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = std::vector<std::pair<long unsigned int, bool> >]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_mk_destructive_iterator(dest_it) const [with Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*, std::pair<const std::vector<unsigned int>, unsigned int>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >; dest_it = spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*, std::pair<const std::vector<unsigned int>, unsigned int>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_begin() [with Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*, std::pair<const std::vector<unsigned int>, unsigned int>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >]'
2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); }
| ^~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_move_from(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = long unsigned int]'
2817 | for (destructive_iterator it = ht.destructive_begin();
| ~~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = long unsigned int]'
2948 | _move_from(mover, ht, min_buckets_wanted);
| ^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_resize_delta(size_type) [with Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = long unsigned int]'
2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
| ^~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::DefaultValue; KT = std::vector<unsigned int>&; Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; value_type = std::pair<const std::vector<unsigned int>, unsigned int>]'
3278 | if (_resize_delta(1))
| ^~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::vector<unsigned int>&; Key = std::vector<unsigned int>; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here
414 | eqID = eqMap[tlist];
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*, std::pair<const std::vector<unsigned int>, unsigned int>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*, std::pair<const std::vector<unsigned int>, unsigned int>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >&)' is deprecated [-Wdeprecated-copy]
2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; }
| ^~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*, std::pair<const std::vector<unsigned int>, unsigned int>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >' has user-provided 'spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>& spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>::operator=(const spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>&) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; row_it = spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*; col_it = std::pair<const std::vector<unsigned int>, unsigned int>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >]'
946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
| ^~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; value_type = std::pair<const std::vector<unsigned int>, unsigned int>; reference = std::pair<const std::vector<unsigned int>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; pointer = std::pair<const std::vector<unsigned int>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; reference = std::pair<const std::vector<unsigned int>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; reference = std::pair<const std::vector<unsigned int>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::DefaultValue; KT = std::vector<unsigned int>&; Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; value_type = std::pair<const std::vector<unsigned int>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::vector<unsigned int>&; Key = std::vector<unsigned int>; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here
414 | eqID = eqMap[tlist];
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >::value_type' {aka 'std::pair<const std::vector<unsigned int>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::vector<unsigned int>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector<unsigned int>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::vector<unsigned int>; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
[ 50%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonExceptions.cpp
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; mutable_value_type = std::pair<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; reference = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; pointer = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; reference = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; reference = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; value_type = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector<std::pair<long unsigned int, bool> >; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; mapped_type = std::vector<std::pair<long unsigned int, bool> >]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here
161 | path[ref_cnt].resize(contigCntPerPath);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >::value_type' {aka 'std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >'} to 'spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >::mutable_reference' {aka 'std::pair<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector<std::pair<long unsigned int, bool> >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = std::vector<std::pair<long unsigned int, bool> >]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; mutable_value_type = std::pair<std::vector<unsigned int>, unsigned int>; reference = std::pair<const std::vector<unsigned int>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; pointer = std::pair<const std::vector<unsigned int>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; reference = std::pair<const std::vector<unsigned int>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; reference = std::pair<const std::vector<unsigned int>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::DefaultValue; KT = std::vector<unsigned int>&; Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; value_type = std::pair<const std::vector<unsigned int>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::vector<unsigned int>&; Key = std::vector<unsigned int>; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here
414 | eqID = eqMap[tlist];
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >::value_type' {aka 'std::pair<const std::vector<unsigned int>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::vector<unsigned int>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector<unsigned int>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::vector<unsigned int>; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
[ 51%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o -MF CMakeFiles/puffer.dir/PufferfishStats.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishStats.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishStats.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishValidate.cpp:15:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 52%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonStringUtils.cpp
[ 53%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -MF CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o.d -o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SimplePosBias.cpp
[ 54%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -MF CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishStats.cpp:16:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SimplePosBias.hpp:4,
from /build/reproducible-path/salmon-1.10.2+ds1/src/SimplePosBias.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 55%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -MF CMakeFiles/salmon_core.dir/SGSmooth.cpp.o.d -o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SGSmooth.cpp
[ 55%] Building CXX object src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -MF CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o.d -o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/install/src/pufferfish/metro/metrohash64.cpp
[ 55%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -MF CMakeFiles/puffer.dir/PufferfishExamine.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishExamine.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30,
from /build/reproducible-path/salmon-1.10.2+ds1/include/UtilityFunctions.hpp:4,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SBModel.hpp:6,
from /build/reproducible-path/salmon-1.10.2+ds1/src/SBModel.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 56%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -MF CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishKmerQuery.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp:14:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishKmerQuery.cpp:13:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp: In function 'std::vector<CanonicalKmer> get_kmers(const std::string&, uint32_t)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp:25:78: warning: unused parameter 'k' [-Wunused-parameter]
25 | std::vector<CanonicalKmer> get_kmers(const std::string& fasta_file, uint32_t k) {
| ~~~~~~~~~^
[ 57%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o -MF CMakeFiles/puffer.dir/FastxParser.cpp.o.d -o CMakeFiles/puffer.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FastxParser.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PuffAligner.hpp:8,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishExamine.cpp:6:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12,
from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonUtils.cpp:18:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 58%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp: In function 'bool alevin::utils::extractBarcode(std::string&, std::string&, ProtocolT&, std::string&) [with ProtocolT = alevin::protocols::SciSeq3; std::string = std::__cxx11::basic_string<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:350:104: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
350 | if (pt.anchorPos != std::string::npos && ( pt.anchorPos == pt.maxHairpinIndexLen || pt.anchorPos == pt.maxHairpinIndexLen -1) // only 2 possible values of pt.anchorPos
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 59%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o -MF CMakeFiles/puffer.dir/PufferFS.cpp.o.d -o CMakeFiles/puffer.dir/PufferFS.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferFS.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30,
from /build/reproducible-path/salmon-1.10.2+ds1/include/Transcript.hpp:8,
from /build/reproducible-path/salmon-1.10.2+ds1/src/DistributionUtils.cpp:3:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 60%] Building C object external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o -MF CMakeFiles/puffer.dir/xxhash.c.o.d -o CMakeFiles/puffer.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/xxhash.c
cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:5,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 61%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o -MF CMakeFiles/puffer.dir/FixFasta.cpp.o.d -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_mk_destructive_iterator(dest_it) const [with Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >*, std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >; dest_it = spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >*, std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_begin() [with Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >*, std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >]'
2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); }
| ^~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_move_from(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = long unsigned int]'
2817 | for (destructive_iterator it = ht.destructive_begin();
| ~~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = long unsigned int]'
2948 | _move_from(mover, ht, min_buckets_wanted);
| ^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_resize_delta(size_type) [with Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = long unsigned int]'
2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
| ^~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; value_type = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >]'
3278 | if (_resize_delta(1))
| ^~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector<std::pair<long unsigned int, bool> >; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; mapped_type = std::vector<std::pair<long unsigned int, bool> >]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here
161 | path[ref_cnt].resize(contigCntPerPath);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >*, std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >*, std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >&)' is deprecated [-Wdeprecated-copy]
2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; }
| ^~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >*, std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >' has user-provided 'spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>& spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>::operator=(const spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>&) [with T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; row_it = spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >*; col_it = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >]'
946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
| ^~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; value_type = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; reference = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; pointer = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; reference = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; reference = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; value_type = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector<std::pair<long unsigned int, bool> >; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; mapped_type = std::vector<std::pair<long unsigned int, bool> >]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here
161 | path[ref_cnt].resize(contigCntPerPath);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >::value_type' {aka 'std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >'} to 'spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >::mutable_reference' {aka 'std::pair<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector<std::pair<long unsigned int, bool> >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = std::vector<std::pair<long unsigned int, bool> >]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_mk_destructive_iterator(dest_it) const [with Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*, std::pair<const std::vector<unsigned int>, unsigned int>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >; dest_it = spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*, std::pair<const std::vector<unsigned int>, unsigned int>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_begin() [with Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*, std::pair<const std::vector<unsigned int>, unsigned int>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >]'
2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); }
| ^~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_move_from(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = long unsigned int]'
2817 | for (destructive_iterator it = ht.destructive_begin();
| ~~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = long unsigned int]'
2948 | _move_from(mover, ht, min_buckets_wanted);
| ^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_resize_delta(size_type) [with Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = long unsigned int]'
2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
| ^~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::DefaultValue; KT = std::vector<unsigned int>&; Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; value_type = std::pair<const std::vector<unsigned int>, unsigned int>]'
3278 | if (_resize_delta(1))
| ^~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::vector<unsigned int>&; Key = std::vector<unsigned int>; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here
414 | eqID = eqMap[tlist];
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*, std::pair<const std::vector<unsigned int>, unsigned int>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*, std::pair<const std::vector<unsigned int>, unsigned int>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >&)' is deprecated [-Wdeprecated-copy]
2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; }
| ^~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*, std::pair<const std::vector<unsigned int>, unsigned int>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >' has user-provided 'spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>& spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>::operator=(const spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>&) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; row_it = spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*; col_it = std::pair<const std::vector<unsigned int>, unsigned int>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >]'
946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
| ^~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; value_type = std::pair<const std::vector<unsigned int>, unsigned int>; reference = std::pair<const std::vector<unsigned int>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; pointer = std::pair<const std::vector<unsigned int>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; reference = std::pair<const std::vector<unsigned int>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; reference = std::pair<const std::vector<unsigned int>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::DefaultValue; KT = std::vector<unsigned int>&; Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; value_type = std::pair<const std::vector<unsigned int>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::vector<unsigned int>&; Key = std::vector<unsigned int>; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here
414 | eqID = eqMap[tlist];
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >::value_type' {aka 'std::pair<const std::vector<unsigned int>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::vector<unsigned int>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector<unsigned int>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::vector<unsigned int>; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
[ 62%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o -MF CMakeFiles/puffer.dir/MemCollector.cpp.o.d -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemCollector.cpp
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; mutable_value_type = std::pair<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; reference = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; pointer = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; reference = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; reference = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; value_type = std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector<std::pair<long unsigned int, bool> >; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > >; mapped_type = std::vector<std::pair<long unsigned int, bool> >]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here
161 | path[ref_cnt].resize(contigCntPerPath);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >::value_type' {aka 'std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >'} to 'spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::pair<long unsigned int, bool> > > > >::mutable_reference' {aka 'std::pair<long unsigned int, std::vector<std::pair<long unsigned int, bool> > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector<std::pair<long unsigned int, bool> >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = std::vector<std::pair<long unsigned int, bool> >]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; mutable_value_type = std::pair<std::vector<unsigned int>, unsigned int>; reference = std::pair<const std::vector<unsigned int>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; pointer = std::pair<const std::vector<unsigned int>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; reference = std::pair<const std::vector<unsigned int>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; reference = std::pair<const std::vector<unsigned int>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::DefaultValue; KT = std::vector<unsigned int>&; Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher>::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; value_type = std::pair<const std::vector<unsigned int>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::vector<unsigned int>&; Key = std::vector<unsigned int>; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, short unsigned int> >&, const std::vector<unsigned int>&)::VecHasher; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here
414 | eqID = eqMap[tlist];
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >::value_type' {aka 'std::pair<const std::vector<unsigned int>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::vector<unsigned int>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector<unsigned int>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::vector<unsigned int>; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:5:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; value_type = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; T = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; T = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; pointer = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; T = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; reference = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Value = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, std::vector<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, std::vector<unsigned int> >::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; reference = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::__cxx11::basic_string<char>, std::vector<unsigned int> >::DefaultValue; KT = std::__cxx11::basic_string<char>&; Value = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, std::vector<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, std::vector<unsigned int> >::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; value_type = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::__cxx11::basic_string<char>&; Key = std::__cxx11::basic_string<char>; T = std::vector<unsigned int>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; mapped_type = std::vector<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:620:34: required from here
620 | txpIdxMap[txpNames[i]].emplace_back(i);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > > >::value_type' {aka 'std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >'} to 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > > >::mutable_reference' {aka 'std::pair<std::__cxx11::basic_string<char>, std::vector<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string<char>; _U2 = std::vector<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::__cxx11::basic_string<char>; _T2 = std::vector<unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; pointer = std::pair<const std::__cxx11::basic_string<char>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string<char>&; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::__cxx11::basic_string<char>&; Key = std::__cxx11::basic_string<char>; T = unsigned int; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:643:33: required from here
643 | geneIdxMap[txpNames[i]] = i;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::value_type' {aka 'std::pair<const std::__cxx11::basic_string<char>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::__cxx11::basic_string<char>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string<char>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::__cxx11::basic_string<char>; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; value_type = std::pair<const unsigned int, unsigned int>; reference = std::pair<const unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; pointer = std::pair<const unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; reference = std::pair<const unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, unsigned int>; Value = std::pair<const unsigned int, unsigned int>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; reference = std::pair<const unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const unsigned int, unsigned int>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; value_type = std::pair<const unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:644:25: required from here
644 | txpToGeneMap[i] = i;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, unsigned int>, spp::libc_allocator<std::pair<const unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const unsigned int, unsigned int>, spp::libc_allocator<std::pair<const unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; mutable_value_type = std::pair<std::__cxx11::basic_string<char>, std::vector<unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; T = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; T = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; T = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; pointer = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; T = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; reference = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Value = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, std::vector<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, std::vector<unsigned int> >::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; reference = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::__cxx11::basic_string<char>, std::vector<unsigned int> >::DefaultValue; KT = std::__cxx11::basic_string<char>&; Value = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, std::vector<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, std::vector<unsigned int> >::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; value_type = std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::__cxx11::basic_string<char>&; Key = std::__cxx11::basic_string<char>; T = std::vector<unsigned int>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > >; mapped_type = std::vector<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:620:34: required from here
620 | txpIdxMap[txpNames[i]].emplace_back(i);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > > >::value_type' {aka 'std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >'} to 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> >, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, std::vector<unsigned int> > > >::mutable_reference' {aka 'std::pair<std::__cxx11::basic_string<char>, std::vector<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string<char>; _U2 = std::vector<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::__cxx11::basic_string<char>; _T2 = std::vector<unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; mutable_value_type = std::pair<std::__cxx11::basic_string<char>, unsigned int>; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; pointer = std::pair<const std::__cxx11::basic_string<char>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string<char>&; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::__cxx11::basic_string<char>&; Key = std::__cxx11::basic_string<char>; T = unsigned int; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:643:33: required from here
643 | geneIdxMap[txpNames[i]] = i;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::value_type' {aka 'std::pair<const std::__cxx11::basic_string<char>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::__cxx11::basic_string<char>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string<char>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::__cxx11::basic_string<char>; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; mutable_value_type = std::pair<unsigned int, unsigned int>; reference = std::pair<const unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; pointer = std::pair<const unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; reference = std::pair<const unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, unsigned int>; Value = std::pair<const unsigned int, unsigned int>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; reference = std::pair<const unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const unsigned int, unsigned int>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; value_type = std::pair<const unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:644:25: required from here
644 | txpToGeneMap[i] = i;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, unsigned int>, spp::libc_allocator<std::pair<const unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const unsigned int, unsigned int>, spp::libc_allocator<std::pair<const unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
[ 62%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o -MF CMakeFiles/puffer.dir/MemChainer.cpp.o.d -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemChainer.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishIndex.hpp:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/MemCollector.hpp:6,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemCollector.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 63%] Linking CXX static library libgraphdump.a
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -P CMakeFiles/graphdump.dir/cmake_clean_target.cmake
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphdump.dir/link.txt --verbose=1
/usr/bin/ar qc libgraphdump.a CMakeFiles/graphdump.dir/graphdump.cpp.o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o
/usr/bin/ranlib libgraphdump.a
make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[ 63%] Built target graphdump
[ 64%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o -MF CMakeFiles/puffer.dir/PuffAligner.cpp.o.d -o CMakeFiles/puffer.dir/PuffAligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PuffAligner.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishIndex.hpp:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/MemChainer.hpp:8,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemChainer.cpp:2:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 65%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -MF CMakeFiles/puffer.dir/PufferfishAligner.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishAligner.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:4:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_mk_destructive_iterator(dest_it) const [with Value = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >*, std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >; dest_it = spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >*, std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_begin() [with Value = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >*, std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >]'
2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); }
| ^~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_move_from(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; size_type = long unsigned int]'
2817 | for (destructive_iterator it = ht.destructive_begin();
| ~~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; size_type = long unsigned int]'
2948 | _move_from(mover, ht, min_buckets_wanted);
| ^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_resize_delta(size_type) [with Value = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; size_type = long unsigned int]'
2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
| ^~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; value_type = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >]'
3278 | if (_resize_delta(1))
| ^~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector<std::__cxx11::basic_string<char> >; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; mapped_type = std::vector<std::__cxx11::basic_string<char> >]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here
264 | duplicateNames[dupInfo.txId].push_back(processedName);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >*, std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >*, std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >&)' is deprecated [-Wdeprecated-copy]
2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; }
| ^~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >*, std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >' has user-provided 'spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>& spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>::operator=(const spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>&) [with T = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; row_it = spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >*; col_it = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >]'
946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
| ^~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; value_type = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; reference = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; T = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; T = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; pointer = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; T = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; reference = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Value = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; reference = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; value_type = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector<std::__cxx11::basic_string<char> >; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; mapped_type = std::vector<std::__cxx11::basic_string<char> >]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here
264 | duplicateNames[dupInfo.txId].push_back(processedName);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >::value_type' {aka 'std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >'} to 'spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >::mutable_reference' {aka 'std::pair<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector<std::__cxx11::basic_string<char> >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = std::vector<std::__cxx11::basic_string<char> >]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_mk_destructive_iterator(dest_it) const [with Value = std::__cxx11::basic_string<char>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_set<std::__cxx11::basic_string<char> >::Identity; SetKey = spp::sparse_hash_set<std::__cxx11::basic_string<char> >::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::__cxx11::basic_string<char> >; destructive_iterator = spp::Two_d_destructive_iterator<std::__cxx11::basic_string<char>, spp::sparsegroup<std::__cxx11::basic_string<char>, spp::libc_allocator<std::__cxx11::basic_string<char> > >*, std::__cxx11::basic_string<char>*, std::input_iterator_tag, spp::libc_allocator<std::__cxx11::basic_string<char> > >; dest_it = spp::Two_d_destructive_iterator<std::__cxx11::basic_string<char>, spp::sparsegroup<std::__cxx11::basic_string<char>, spp::libc_allocator<std::__cxx11::basic_string<char> > >*, std::__cxx11::basic_string<char>*, std::input_iterator_tag, spp::libc_allocator<std::__cxx11::basic_string<char> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_begin() [with Value = std::__cxx11::basic_string<char>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_set<std::__cxx11::basic_string<char> >::Identity; SetKey = spp::sparse_hash_set<std::__cxx11::basic_string<char> >::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::__cxx11::basic_string<char> >; destructive_iterator = spp::Two_d_destructive_iterator<std::__cxx11::basic_string<char>, spp::sparsegroup<std::__cxx11::basic_string<char>, spp::libc_allocator<std::__cxx11::basic_string<char> > >*, std::__cxx11::basic_string<char>*, std::input_iterator_tag, spp::libc_allocator<std::__cxx11::basic_string<char> > >]'
2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); }
| ^~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_move_from(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::__cxx11::basic_string<char>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_set<std::__cxx11::basic_string<char> >::Identity; SetKey = spp::sparse_hash_set<std::__cxx11::basic_string<char> >::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::__cxx11::basic_string<char> >; size_type = long unsigned int]'
2817 | for (destructive_iterator it = ht.destructive_begin();
| ~~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::__cxx11::basic_string<char>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_set<std::__cxx11::basic_string<char> >::Identity; SetKey = spp::sparse_hash_set<std::__cxx11::basic_string<char> >::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::__cxx11::basic_string<char> >; size_type = long unsigned int]'
2948 | _move_from(mover, ht, min_buckets_wanted);
| ^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_resize_delta(size_type) [with Value = std::__cxx11::basic_string<char>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_set<std::__cxx11::basic_string<char> >::Identity; SetKey = spp::sparse_hash_set<std::__cxx11::basic_string<char> >::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::__cxx11::basic_string<char> >; size_type = long unsigned int]'
2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
| ^~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3234:9: required from 'std::pair<typename spp::sparsetable<Value, Alloc>::ne_iterator, bool> spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::insert(P&&) [with P = std::__cxx11::basic_string<char>&; Value = std::__cxx11::basic_string<char>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_set<std::__cxx11::basic_string<char> >::Identity; SetKey = spp::sparse_hash_set<std::__cxx11::basic_string<char> >::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::__cxx11::basic_string<char> >; typename spp::sparsetable<Value, Alloc>::ne_iterator = spp::Two_d_iterator<std::__cxx11::basic_string<char>, spp::sparsegroup<std::__cxx11::basic_string<char>, spp::libc_allocator<std::__cxx11::basic_string<char> > >*, std::__cxx11::basic_string<char>*, std::bidirectional_iterator_tag>]'
3234 | _resize_delta(1); // adding an object, grow if need be
| ^~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:4225:73: required from 'std::pair<typename spp::sparse_hashtable<Value, Value, HashFcn, spp::sparse_hash_set<Value, HashFcn, EqualKey, Alloc>::Identity, spp::sparse_hash_set<Value, HashFcn, EqualKey, Alloc>::SetKey, EqualKey, Alloc>::const_iterator, bool> spp::sparse_hash_set<Value, HashFcn, EqualKey, Alloc>::insert(P&&) [with P = std::__cxx11::basic_string<char>&; Value = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::__cxx11::basic_string<char> >; typename spp::sparse_hashtable<Value, Value, HashFcn, Identity, SetKey, EqualKey, Alloc>::const_iterator = spp::Two_d_iterator<const std::__cxx11::basic_string<char>, const spp::sparsegroup<std::__cxx11::basic_string<char>, spp::libc_allocator<std::__cxx11::basic_string<char> > >*, const std::__cxx11::basic_string<char>*, std::bidirectional_iterator_tag>]'
4225 | std::pair<iterator, bool> insert(P&& obj) { return rep.insert(std::forward<P>(obj)); }
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:490:26: required from here
490 | auto it = dset.insert(dname);
| ~~~~~~~~~~~^~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator<std::__cxx11::basic_string<char>, spp::sparsegroup<std::__cxx11::basic_string<char>, spp::libc_allocator<std::__cxx11::basic_string<char> > >*, std::__cxx11::basic_string<char>*, std::input_iterator_tag, spp::libc_allocator<std::__cxx11::basic_string<char> > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator<std::__cxx11::basic_string<char>, spp::sparsegroup<std::__cxx11::basic_string<char>, spp::libc_allocator<std::__cxx11::basic_string<char> > >*, std::__cxx11::basic_string<char>*, std::input_iterator_tag, spp::libc_allocator<std::__cxx11::basic_string<char> > >&)' is deprecated [-Wdeprecated-copy]
2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; }
| ^~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator<std::__cxx11::basic_string<char>, spp::sparsegroup<std::__cxx11::basic_string<char>, spp::libc_allocator<std::__cxx11::basic_string<char> > >*, std::__cxx11::basic_string<char>*, std::input_iterator_tag, spp::libc_allocator<std::__cxx11::basic_string<char> > >' has user-provided 'spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>& spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>::operator=(const spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>&) [with T = std::__cxx11::basic_string<char>; row_it = spp::sparsegroup<std::__cxx11::basic_string<char>, spp::libc_allocator<std::__cxx11::basic_string<char> > >*; col_it = std::__cxx11::basic_string<char>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator<std::__cxx11::basic_string<char> >]'
946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
| ^~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; mutable_value_type = std::pair<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; reference = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; T = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; T = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; T = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; pointer = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; T = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; reference = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Value = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; reference = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; value_type = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector<std::__cxx11::basic_string<char> >; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; mapped_type = std::vector<std::__cxx11::basic_string<char> >]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here
264 | duplicateNames[dupInfo.txId].push_back(processedName);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >::value_type' {aka 'std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >'} to 'spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >::mutable_reference' {aka 'std::pair<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector<std::__cxx11::basic_string<char> >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = std::vector<std::__cxx11::basic_string<char> >]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PuffAligner.hpp:8,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PuffAligner.cpp:2:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishAligner.cpp:35:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 66%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -MF CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o.d -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mutable_value_type = std::pair<long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
[ 67%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -MF CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o.d -o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/LibraryFormat.cpp
[ 68%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -MF CMakeFiles/puffer.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/metro/metrohash64.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/RefSeqConstructor.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/RefSeqConstructor.hpp:5:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_mk_destructive_iterator(dest_it) const [with Value = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >*, std::pair<const unsigned int, pufferfish::util::ContigBlock>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >; dest_it = spp::Two_d_destructive_iterator<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >*, std::pair<const unsigned int, pufferfish::util::ContigBlock>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_begin() [with Value = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >*, std::pair<const unsigned int, pufferfish::util::ContigBlock>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >]'
2607 | destructive_iterator destructive_begin() { return _mk_destructive_iterator(table.destructive_begin()); }
| ^~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2817:43: required from 'void spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_move_from(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; size_type = long unsigned int]'
2817 | for (destructive_iterator it = ht.destructive_begin();
| ~~~^~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; size_type = long unsigned int]'
2948 | _move_from(mover, ht, min_buckets_wanted);
| ^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2745:26: required from 'bool spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_resize_delta(size_type) [with Value = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; size_type = long unsigned int]'
2745 | sparse_hashtable tmp(MoveDontCopy, *this, resize_to);
| ^~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3278:21: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::DefaultValue; KT = long unsigned int&; Value = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; value_type = std::pair<const unsigned int, pufferfish::util::ContigBlock>]'
3278 | if (_resize_delta(1))
| ^~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; mapped_type = pufferfish::util::ContigBlock]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor<PufferfishIndexT>::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>]'
143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid];
| ~~~~~~~~~~~~~~~~~~^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here
466 | template class RefSeqConstructor<PufferfishIndex>;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2632:78: warning: implicitly-declared 'constexpr spp::Two_d_destructive_iterator<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >*, std::pair<const unsigned int, pufferfish::util::ContigBlock>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >*, std::pair<const unsigned int, pufferfish::util::ContigBlock>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >&)' is deprecated [-Wdeprecated-copy]
2632 | destructive_iterator _mk_destructive_iterator(dest_it it) const { return it; }
| ^~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >*, std::pair<const unsigned int, pufferfish::util::ContigBlock>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >' has user-provided 'spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>& spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>::operator=(const spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>&) [with T = std::pair<const unsigned int, pufferfish::util::ContigBlock>; row_it = spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >*; col_it = std::pair<const unsigned int, pufferfish::util::ContigBlock>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >]'
946 | Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
| ^~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; value_type = std::pair<const unsigned int, pufferfish::util::ContigBlock>; reference = std::pair<const unsigned int, pufferfish::util::ContigBlock>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, pufferfish::util::ContigBlock>; T = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, pufferfish::util::ContigBlock>; T = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; pointer = std::pair<const unsigned int, pufferfish::util::ContigBlock>*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, pufferfish::util::ContigBlock>; T = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; reference = std::pair<const unsigned int, pufferfish::util::ContigBlock>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Value = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; reference = std::pair<const unsigned int, pufferfish::util::ContigBlock>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::DefaultValue; KT = long unsigned int&; Value = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; value_type = std::pair<const unsigned int, pufferfish::util::ContigBlock>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; mapped_type = pufferfish::util::ContigBlock]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor<PufferfishIndexT>::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>]'
143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid];
| ~~~~~~~~~~~~~~~~~~^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here
466 | template class RefSeqConstructor<PufferfishIndex>;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::value_type' {aka 'std::pair<const unsigned int, pufferfish::util::ContigBlock>'} to 'spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::mutable_reference' {aka 'std::pair<unsigned int, pufferfish::util::ContigBlock>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = pufferfish::util::ContigBlock; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = pufferfish::util::ContigBlock]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; mutable_value_type = std::pair<unsigned int, pufferfish::util::ContigBlock>; reference = std::pair<const unsigned int, pufferfish::util::ContigBlock>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, pufferfish::util::ContigBlock>; T = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, pufferfish::util::ContigBlock>; T = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, pufferfish::util::ContigBlock>; T = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; pointer = std::pair<const unsigned int, pufferfish::util::ContigBlock>*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, pufferfish::util::ContigBlock>; T = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; reference = std::pair<const unsigned int, pufferfish::util::ContigBlock>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Value = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; reference = std::pair<const unsigned int, pufferfish::util::ContigBlock>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::DefaultValue; KT = long unsigned int&; Value = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; value_type = std::pair<const unsigned int, pufferfish::util::ContigBlock>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; mapped_type = pufferfish::util::ContigBlock]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor<PufferfishIndexT>::doDFS(size_t, size_t, bool, pufferfish::util::ContigBlock&, uint32_t, pufferfish::util::ContigBlock&, bool, uint32_t, bool, std::string&, bool) [with PufferfishIndexT = PufferfishIndex; size_t = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>]'
143 | pufferfish::util::ContigBlock& cb = (*contigSeqCache_)[c.cid];
| ~~~~~~~~~~~~~~~~~~^
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here
466 | template class RefSeqConstructor<PufferfishIndex>;
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::value_type' {aka 'std::pair<const unsigned int, pufferfish::util::ContigBlock>'} to 'spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >::mutable_reference' {aka 'std::pair<unsigned int, pufferfish::util::ContigBlock>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = pufferfish::util::ContigBlock; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = pufferfish::util::ContigBlock]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
[ 69%] Linking CXX static library libalevin_core.a
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1
"/usr/bin/gcc-ar-14" qc libalevin_core.a CMakeFiles/alevin_core.dir/edlib.cpp.o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o
"/usr/bin/gcc-ranlib-14" libalevin_core.a
make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[ 69%] Built target alevin_core
[ 70%] Linking CXX static library libsalmon_core.a
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1
"/usr/bin/gcc-ar-14" qc libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o CMakeFiles/salmon_core.dir/backtrace.cc.o CMakeFiles/salmon_core.dir/xxhash.c.o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o CMakeFiles/salmon_core.dir/SBModel.cpp.o CMakeFiles/salmon_core.dir/FastxParser.cpp.o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o
"/usr/bin/gcc-ranlib-14" libsalmon_core.a
make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[ 70%] Built target salmon_core
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/sha2.hpp:9,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/digestpp.hpp:6,
from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:27:
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]',
inlined from 'digestpp::detail::sha2_provider<long unsigned int, 0>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<long unsigned int, 0>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<long unsigned int, 0>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:537:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript 'const long unsigned int[0]' is partly outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/digestpp.hpp:5:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript 'const unsigned int[0]' is partly outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [1, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 4 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [2, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 8 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [3, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 12 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [4, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 16 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [5, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 20 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [6, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 24 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [7, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 28 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [8, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 32 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [9, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 36 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [10, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 40 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [11, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 44 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [12, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 48 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [13, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 52 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [14, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 56 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
In member function 'void digestpp::detail::sha2_provider<T, O>::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]',
inlined from 'digestpp::detail::sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:169:61,
inlined from 'void digestpp::detail::absorb_bytes(const unsigned char*, size_t, size_t, size_t, unsigned char*, size_t&, T&, TF) [with T = long unsigned int; TF = sha2_provider<unsigned int, 256>::update(const unsigned char*, size_t)::<lambda(const unsigned char*, size_t)>]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/../../detail/absorb_data.hpp:32:12,
inlined from 'void digestpp::detail::sha2_provider<T, O>::update(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:168:23,
inlined from 'digestpp::hasher<HashProvider, Mixin>& digestpp::hasher<HashProvider, Mixin>::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >; HashProvider = digestpp::detail::sha2_provider<unsigned int, 256>; Mixin = digestpp::mixin::null_mixin]' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19,
inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:536:26:
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp:208:48: warning: array subscript [15, 2305843009213693951] is outside array bounds of 'unsigned char [1]' [-Warray-bounds=]
208 | M[i] = byteswap(reinterpret_cast<const T*>(data)[blk * 16 + i]);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)':
/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/hasher.hpp:169:39: note: at offset 60 into object 'byte' of size 1
169 | unsigned char byte = *begin++;
| ^~~~
[ 71%] Linking CXX static library libUnitTestsMain.a
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cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/UnitTestsMain.dir/link.txt --verbose=1
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make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
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make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/depend
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[ 72%] Building CXX object src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp
[ 73%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -MF CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o.d -o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/install/src/pufferfish/rank9b.cpp
[ 74%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o -MF CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o.d -o CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/tests/GCSampleTests.cpp
[ 75%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -MF CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o.d -o CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/tests/LibraryTypeTests.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30,
from /build/reproducible-path/salmon-1.10.2+ds1/tests/LibraryTypeTests.cpp:6:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30,
from /build/reproducible-path/salmon-1.10.2+ds1/tests/GCSampleTests.cpp:6:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30,
from /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp:12:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 76%] Linking CXX static library libpuffer.a
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/puffer.dir/cmake_clean_target.cmake
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/puffer.dir/link.txt --verbose=1
/usr/bin/ar qc libpuffer.a CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o CMakeFiles/puffer.dir/edlib.cpp.o CMakeFiles/puffer.dir/Util.cpp.o CMakeFiles/puffer.dir/rank9sel.cpp.o CMakeFiles/puffer.dir/rank9b.cpp.o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o CMakeFiles/puffer.dir/PufferfishStats.cpp.o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o CMakeFiles/puffer.dir/FastxParser.cpp.o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o CMakeFiles/puffer.dir/PufferFS.cpp.o CMakeFiles/puffer.dir/xxhash.c.o CMakeFiles/puffer.dir/FixFasta.cpp.o CMakeFiles/puffer.dir/MemCollector.cpp.o CMakeFiles/puffer.dir/MemChainer.cpp.o CMakeFiles/puffer.dir/PuffAligner.cpp.o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o
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/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/unitTests.dir/link.d CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -o unitTests -L/build/reproducible-path/salmon-1.10.2+ds1/lib -L/build/reproducible-path/salmon-1.10.2+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex libsalmon_core.a libalevin_core.a -lgff libUnitTestsMain.a /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_timer.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libstaden-read.so /usr/lib/x86_64-linux-gnu/libhtscodecs.so /usr/lib/x86_64-linux-gnu/libcurl.so -lz -lm -llzma -lbz2 -ltbb -ltbbmalloc -lgomp -lrt -ldl /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0
Copying unitTests
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E copy /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src/unitTests /build/reproducible-path/salmon-1.10.2+ds1/tests/unitTests
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[ 78%] Linking CXX static library libtwopaco.a
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -P CMakeFiles/twopaco.dir/cmake_clean_target.cmake
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -E cmake_link_script CMakeFiles/twopaco.dir/link.txt --verbose=1
/usr/bin/ar qc libtwopaco.a CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o CMakeFiles/twopaco.dir/constructor.cpp.o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o CMakeFiles/twopaco.dir/compressedstring.cpp.o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o CMakeFiles/twopaco.dir/test.cpp.o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o CMakeFiles/twopaco.dir/common.cpp.o
/usr/bin/ranlib libtwopaco.a
make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
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make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/depend
make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[ 79%] Building CXX object src/CMakeFiles/salmon.dir/EMUtils.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/EMUtils.cpp.o -MF CMakeFiles/salmon.dir/EMUtils.cpp.o.d -o CMakeFiles/salmon.dir/EMUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/EMUtils.cpp
[ 80%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o -MF CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o.d -o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedEMOptimizer.cpp
[ 81%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o -MF CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o.d -o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedGibbsSampler.cpp
[ 81%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o
[ 82%] Building CXX object src/CMakeFiles/salmon.dir/Salmon.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o -MF CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o.d -o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp
[ 83%] Building CXX object src/CMakeFiles/salmon.dir/Graph.cpp.o
[ 84%] Building CXX object src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/Salmon.cpp.o -MF CMakeFiles/salmon.dir/Salmon.cpp.o.d -o CMakeFiles/salmon.dir/Salmon.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/Salmon.cpp
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o -MF CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o.d -o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/BuildSalmonIndex.cpp
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/Graph.cpp.o -MF CMakeFiles/salmon.dir/Graph.cpp.o.d -o CMakeFiles/salmon.dir/Graph.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/Graph.cpp
[ 85%] Building CXX object src/CMakeFiles/salmon.dir/DedupUMI.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/DedupUMI.cpp.o -MF CMakeFiles/salmon.dir/DedupUMI.cpp.o.d -o CMakeFiles/salmon.dir/DedupUMI.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp
[ 86%] Building CXX object src/CMakeFiles/salmon.dir/Alevin.cpp.o
[ 87%] Building CXX object src/CMakeFiles/salmon.dir/AlevinHash.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/Alevin.cpp.o -MF CMakeFiles/salmon.dir/Alevin.cpp.o.d -o CMakeFiles/salmon.dir/Alevin.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/AlevinHash.cpp.o -MF CMakeFiles/salmon.dir/AlevinHash.cpp.o.d -o CMakeFiles/salmon.dir/AlevinHash.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp
[ 87%] Building CXX object src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o
[ 89%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o
[ 88%] Building CXX object src/CMakeFiles/salmon.dir/WhiteList.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -MF CMakeFiles/salmon.dir/SalmonAlevin.cpp.o.d -o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/WhiteList.cpp.o -MF CMakeFiles/salmon.dir/WhiteList.cpp.o.d -o CMakeFiles/salmon.dir/WhiteList.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/WhiteList.cpp
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantify.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantify.cpp
[ 90%] Building CXX object src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp
[ 91%] Building CXX object src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -MF CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o.d -o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentStartPositionDistribution.cpp
[ 92%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o
[ 93%] Building CXX object src/CMakeFiles/salmon.dir/GZipWriter.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantMerge.cpp
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/GZipWriter.cpp.o -MF CMakeFiles/salmon.dir/GZipWriter.cpp.o.d -o CMakeFiles/salmon.dir/GZipWriter.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/GZipWriter.cpp
[ 94%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o
[ 95%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o
[ 95%] Building CXX object src/CMakeFiles/salmon.dir/FASTAParser.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/FASTAParser.cpp.o -MF CMakeFiles/salmon.dir/FASTAParser.cpp.o.d -o CMakeFiles/salmon.dir/FASTAParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FASTAParser.cpp
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -MF CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o.d -o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/ProgramOptionsGenerator.cpp
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o -MF CMakeFiles/salmon.dir/AlignmentModel.cpp.o.d -o CMakeFiles/salmon.dir/AlignmentModel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/pcg_random.hpp:104,
from /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedGibbsSampler.cpp:22:
/build/reproducible-path/salmon-1.10.2+ds1/include/pcg_extras.hpp:563:51: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
563 | fnv(IntType(2166136261U ^ sizeof(IntType)), __DATE__ __TIME__ __FILE__);
| ^~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/pcg_extras.hpp:563:60: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
563 | fnv(IntType(2166136261U ^ sizeof(IntType)), __DATE__ __TIME__ __FILE__);
| ^~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/include/ProgramOptionsGenerator.hpp:5,
from /build/reproducible-path/salmon-1.10.2+ds1/src/ProgramOptionsGenerator.cpp:4:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinOpts.hpp:5,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SingleCellProtocols.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/include/WhiteList.hpp:14,
from /build/reproducible-path/salmon-1.10.2+ds1/src/WhiteList.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 96%] Building CXX object src/CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o -MF CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o.d -o CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentCommon.hpp:10,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentModel.hpp:6,
from /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:8:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/src/FASTAParser.cpp:11:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantMerge.cpp:29:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinHash.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12,
from /build/reproducible-path/salmon-1.10.2+ds1/src/GZipWriter.cpp:9:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:27,
from /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:8,
from /build/reproducible-path/salmon-1.10.2+ds1/src/Graph.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:27,
from /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:8,
from /build/reproducible-path/salmon-1.10.2+ds1/include/DedupUMI.hpp:4,
from /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonIndex.hpp:11,
from /build/reproducible-path/salmon-1.10.2+ds1/src/Salmon.cpp:49:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:48:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30,
from /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp:12:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12,
from /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedEMOptimizer.cpp:22:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30,
from /build/reproducible-path/salmon-1.10.2+ds1/include/Transcript.hpp:8,
from /build/reproducible-path/salmon-1.10.2+ds1/include/EMUtils.hpp:6,
from /build/reproducible-path/salmon-1.10.2+ds1/src/EMUtils.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonIndex.hpp:11,
from /build/reproducible-path/salmon-1.10.2+ds1/src/BuildSalmonIndex.cpp:34:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantify.cpp:75:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
[ 97%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -MF CMakeFiles/salmon.dir/AlignmentCommon.cpp.o.d -o CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentCommon.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12,
from /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedGibbsSampler.cpp:30:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:76:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/ONTAlignmentModel.hpp:9,
from /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:11:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp: In member function 'AlignmentModel::AlnModelProb AlignmentModel::logLikelihood(bam_seq_t*, bam_seq_t*, Transcript&, std::vector<AtomicMatrix<double> >&)':
/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:96:33: warning: unused parameter 'primary' [-Wunused-parameter]
96 | bam_seq_t* read, bam_seq_t* primary, Transcript& ref,
| ~~~~~~~~~~~^~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp: In member function 'double AlignmentModel::logLikelihood(const ReadPair&, const ReadPair&, Transcript&)':
/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:230:75: warning: unused parameter 'primary' [-Wunused-parameter]
230 | double AlignmentModel::logLikelihood(const ReadPair& hit, const ReadPair& primary, Transcript& ref) {
| ~~~~~~~~~~~~~~~~^~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp: In member function 'void AlignmentModel::update(const ReadPair&, const ReadPair&, Transcript&, double, double)':
/build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentModel.cpp:429:66: warning: unused parameter 'primary' [-Wunused-parameter]
429 | void AlignmentModel::update(const ReadPair& hit, const ReadPair& primary,
| ~~~~~~~~~~~~~~~~^~~~~~~
[ 98%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantifyAlignments.cpp
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30,
from /build/reproducible-path/salmon-1.10.2+ds1/include/Transcript.hpp:8,
from /build/reproducible-path/salmon-1.10.2+ds1/include/ClusterForest.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadExperiment.hpp:5,
from /build/reproducible-path/salmon-1.10.2+ds1/include/CollapsedCellOptimizer.hpp:11,
from /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:5:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentCommon.hpp:10,
from /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentCommon.cpp:1:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; value_type = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; reference = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; pointer = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; reference = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; reference = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::DefaultValue; KT = std::pair<unsigned int, unsigned int>&; Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; value_type = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::pair<unsigned int, unsigned int>&; Key = std::pair<unsigned int, unsigned int>; T = unsigned int; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Graph.cpp:10:29: required from here
10 | index = vertMap[node];
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> > >::value_type' {aka 'std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::pair<unsigned int, unsigned int>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair<unsigned int, unsigned int>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::pair<unsigned int, unsigned int>; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:65:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h: In instantiation of 'T* spp::libc_allocator<T>::reallocate(pointer, size_t) [with T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; pointer = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>*; size_t = long unsigned int]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1383:38: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1383 | _group = alloc.reallocate(_group, num_alloc);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; pointer = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; reference = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; reference = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::DefaultValue; KT = std::pair<unsigned int, unsigned int>&; Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; value_type = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::pair<unsigned int, unsigned int>&; Key = std::pair<unsigned int, unsigned int>; T = unsigned int; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Graph.cpp:10:29: required from here
10 | index = vertMap[node];
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h:425:51: warning: 'void* realloc(void*, size_t)' moving an object of non-trivially copyable type 'struct std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>'; use 'new' and 'delete' instead [-Wclass-memaccess]
425 | pointer res = static_cast<pointer>(realloc(p, new_size * sizeof(T)));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_algobase.h:64,
from /usr/include/c++/14/string:51,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/streambuf:43,
from /usr/include/c++/14/bits/streambuf_iterator.h:35,
from /usr/include/c++/14/iterator:66,
from /usr/include/boost/graph/graph_traits.hpp:14,
from /usr/include/boost/graph/depth_first_search.hpp:17,
from /usr/include/boost/graph/connected_components.hpp:15,
from /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:4:
/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'struct std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>' declared here
284 | struct pair
| ^~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; mutable_value_type = std::pair<std::pair<unsigned int, unsigned int>, unsigned int>; reference = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; pointer = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; reference = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; reference = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::DefaultValue; KT = std::pair<unsigned int, unsigned int>&; Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; value_type = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::pair<unsigned int, unsigned int>&; Key = std::pair<unsigned int, unsigned int>; T = unsigned int; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Graph.cpp:10:29: required from here
10 | index = vertMap[node];
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> > >::value_type' {aka 'std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::pair<unsigned int, unsigned int>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair<unsigned int, unsigned int>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::pair<unsigned int, unsigned int>; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
[ 99%] Building CXX object src/CMakeFiles/salmon.dir/BAMUtils.cpp.o
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/BAMUtils.cpp.o -MF CMakeFiles/salmon.dir/BAMUtils.cpp.o.d -o CMakeFiles/salmon.dir/BAMUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/BAMUtils.cpp
/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In constructor 'ONTAlignmentModel::ONTAlignmentModel(double, uint32_t)':
/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:17:45: warning: unused parameter 'alpha' [-Wunused-parameter]
17 | ONTAlignmentModel::ONTAlignmentModel(double alpha, uint32_t readBins)
| ~~~~~~~^~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function 'double ONTAlignmentModel::logLikelihood(const UnpairedRead&, const UnpairedRead&, Transcript&)':
/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:53:22: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare]
53 | if(counts.sclips() >= cigarRLen)
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function 'void ONTAlignmentModel::update(const UnpairedRead&, const UnpairedRead&, Transcript&, double, double)':
/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:137:56: warning: unused parameter 'p' [-Wunused-parameter]
137 | Transcript& ref, double p, double mass) {
| ~~~~~~~^
/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function 'void ONTAlignmentModel::printModel(std::ostream&)':
/build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:194:50: warning: unused parameter 'os' [-Wunused-parameter]
194 | void ONTAlignmentModel::printModel(std::ostream& os) {
| ~~~~~~~~~~~~~~^~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mutable_value_type = std::pair<long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:60:
/build/reproducible-path/salmon-1.10.2+ds1/include/BarcodeModel.hpp: In function 'void alevin::model::coinTossBarcodeModel(std::string, const std::vector<std::__cxx11::basic_string<char> >&, MapT&)':
/build/reproducible-path/salmon-1.10.2+ds1/include/BarcodeModel.hpp:168:31: warning: loop variable 'trueBarcode' creates a copy from type 'const std::string' {aka 'const std::__cxx11::basic_string<char>'} [-Wrange-loop-construct]
168 | for(const std::string trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/BarcodeModel.hpp:168:31: note: use reference type to prevent copying
168 | for(const std::string trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mutable_value_type = std::pair<long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; value_type = std::pair<const unsigned int, std::vector<unsigned int> >; reference = std::pair<const unsigned int, std::vector<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, std::vector<unsigned int> >; T = std::pair<const unsigned int, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, std::vector<unsigned int> >; T = std::pair<const unsigned int, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; pointer = std::pair<const unsigned int, std::vector<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, std::vector<unsigned int> >; T = std::pair<const unsigned int, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; reference = std::pair<const unsigned int, std::vector<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, std::vector<unsigned int> >; Value = std::pair<const unsigned int, std::vector<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, std::vector<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, std::vector<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; reference = std::pair<const unsigned int, std::vector<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, std::vector<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, std::vector<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, std::vector<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, std::vector<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; value_type = std::pair<const unsigned int, std::vector<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = std::vector<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; mapped_type = std::vector<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:32:17: required from here
32 | tidMap[txp].emplace_back(eqId);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, std::vector<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, std::vector<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, std::vector<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, std::vector<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = std::vector<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = std::vector<unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; value_type = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; reference = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; T = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; T = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; pointer = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >*; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; T = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; reference = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Value = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Key = std::vector<unsigned int>; HashFcn = boost::hash<std::vector<unsigned int> >; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >, boost::hash<std::vector<unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >, boost::hash<std::vector<unsigned int> > >::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; reference = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >, boost::hash<std::vector<unsigned int> > >::DefaultValue; KT = std::vector<unsigned int>&; Value = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Key = std::vector<unsigned int>; HashFcn = boost::hash<std::vector<unsigned int> >; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >, boost::hash<std::vector<unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >, boost::hash<std::vector<unsigned int> > >::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; value_type = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::vector<unsigned int>&; Key = std::vector<unsigned int>; T = std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >; HashFcn = boost::hash<std::vector<unsigned int> >; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; mapped_type = std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:285:29: required from here
285 | eqclassHash[genesVec].first += 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > > >::value_type' {aka 'std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >'} to 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > > >::mutable_reference' {aka 'std::pair<std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector<unsigned int>; _U2 = std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::vector<unsigned int>; _T2 = std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const short unsigned int, short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; value_type = std::pair<const short unsigned int, short unsigned int>; reference = std::pair<const short unsigned int, short unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const short unsigned int, short unsigned int>; T = std::pair<const short unsigned int, short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const short unsigned int, short unsigned int>; T = std::pair<const short unsigned int, short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; pointer = std::pair<const short unsigned int, short unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const short unsigned int, short unsigned int>; T = std::pair<const short unsigned int, short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; reference = std::pair<const short unsigned int, short unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const short unsigned int, short unsigned int>; Value = std::pair<const short unsigned int, short unsigned int>; Key = short unsigned int; HashFcn = spp::spp_hash<short unsigned int>; ExtractKey = spp::sparse_hash_map<short unsigned int, short unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<short unsigned int, short unsigned int>::SetKey; EqualKey = std::equal_to<short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; reference = std::pair<const short unsigned int, short unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<short unsigned int, short unsigned int>::DefaultValue; KT = short unsigned int&; Value = std::pair<const short unsigned int, short unsigned int>; Key = short unsigned int; HashFcn = spp::spp_hash<short unsigned int>; ExtractKey = spp::sparse_hash_map<short unsigned int, short unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<short unsigned int, short unsigned int>::SetKey; EqualKey = std::equal_to<short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; value_type = std::pair<const short unsigned int, short unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = short unsigned int&; Key = short unsigned int; T = short unsigned int; HashFcn = spp::spp_hash<short unsigned int>; EqualKey = std::equal_to<short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; mapped_type = short unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:286:47: required from here
286 | eqclassHash[genesVec].second[readspmol] += 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const short unsigned int, short unsigned int>, spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> > >::value_type' {aka 'std::pair<const short unsigned int, short unsigned int>'} to 'spp::sparsegroup<std::pair<const short unsigned int, short unsigned int>, spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> > >::mutable_reference' {aka 'std::pair<short unsigned int, short unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = short unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = short unsigned int; _T2 = short unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; value_type = std::pair<const std::vector<unsigned int>, unsigned int>; reference = std::pair<const std::vector<unsigned int>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; pointer = std::pair<const std::vector<unsigned int>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; reference = std::pair<const std::vector<unsigned int>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = boost::hash<std::vector<unsigned int> >; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, boost::hash<std::vector<unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, boost::hash<std::vector<unsigned int> > >::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; reference = std::pair<const std::vector<unsigned int>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, boost::hash<std::vector<unsigned int> > >::DefaultValue; KT = std::vector<unsigned int>&; Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = boost::hash<std::vector<unsigned int> >; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, boost::hash<std::vector<unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, boost::hash<std::vector<unsigned int> > >::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; value_type = std::pair<const std::vector<unsigned int>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::vector<unsigned int>&; Key = std::vector<unsigned int>; T = unsigned int; HashFcn = boost::hash<std::vector<unsigned int> >; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:413:29: required from here
413 | eqclassHash[genesVec] += 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >::value_type' {aka 'std::pair<const std::vector<unsigned int>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::vector<unsigned int>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector<unsigned int>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::vector<unsigned int>; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; value_type = std::pair<const unsigned int, unsigned int>; reference = std::pair<const unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; pointer = std::pair<const unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; reference = std::pair<const unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, unsigned int>; Value = std::pair<const unsigned int, unsigned int>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; reference = std::pair<const unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, unsigned int>::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, unsigned int>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; value_type = std::pair<const unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:477:29: required from here
477 | vertexIndices[gene] = gid;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, unsigned int>, spp::libc_allocator<std::pair<const unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const unsigned int, unsigned int>, spp::libc_allocator<std::pair<const unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mutable_value_type = std::pair<long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinHash.hpp:10:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; mutable_value_type = std::pair<unsigned int, std::vector<unsigned int> >; reference = std::pair<const unsigned int, std::vector<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, std::vector<unsigned int> >; T = std::pair<const unsigned int, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, std::vector<unsigned int> >; T = std::pair<const unsigned int, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, std::vector<unsigned int> >; T = std::pair<const unsigned int, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; pointer = std::pair<const unsigned int, std::vector<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, std::vector<unsigned int> >; T = std::pair<const unsigned int, std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; reference = std::pair<const unsigned int, std::vector<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, std::vector<unsigned int> >; Value = std::pair<const unsigned int, std::vector<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, std::vector<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, std::vector<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; reference = std::pair<const unsigned int, std::vector<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, std::vector<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, std::vector<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, std::vector<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, std::vector<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; value_type = std::pair<const unsigned int, std::vector<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = std::vector<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > >; mapped_type = std::vector<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:32:17: required from here
32 | tidMap[txp].emplace_back(eqId);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, std::vector<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, std::vector<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, std::vector<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, std::vector<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, std::vector<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = std::vector<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = std::vector<unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; mutable_value_type = std::pair<std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; reference = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; T = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; T = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; T = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; pointer = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >*; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; T = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; reference = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Value = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Key = std::vector<unsigned int>; HashFcn = boost::hash<std::vector<unsigned int> >; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >, boost::hash<std::vector<unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >, boost::hash<std::vector<unsigned int> > >::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; reference = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >, boost::hash<std::vector<unsigned int> > >::DefaultValue; KT = std::vector<unsigned int>&; Value = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >; Key = std::vector<unsigned int>; HashFcn = boost::hash<std::vector<unsigned int> >; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >, boost::hash<std::vector<unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >, boost::hash<std::vector<unsigned int> > >::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; value_type = std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::vector<unsigned int>&; Key = std::vector<unsigned int>; T = std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >; HashFcn = boost::hash<std::vector<unsigned int> >; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > >; mapped_type = std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:285:29: required from here
285 | eqclassHash[genesVec].first += 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > > >::value_type' {aka 'std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >'} to 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >, spp::libc_allocator<std::pair<const std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > > > >::mutable_reference' {aka 'std::pair<std::vector<unsigned int>, std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector<unsigned int>; _U2 = std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::vector<unsigned int>; _T2 = std::pair<unsigned int, spp::sparse_hash_map<short unsigned int, short unsigned int> >]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const short unsigned int, short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; mutable_value_type = std::pair<short unsigned int, short unsigned int>; reference = std::pair<const short unsigned int, short unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const short unsigned int, short unsigned int>; T = std::pair<const short unsigned int, short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const short unsigned int, short unsigned int>; T = std::pair<const short unsigned int, short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const short unsigned int, short unsigned int>; T = std::pair<const short unsigned int, short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; pointer = std::pair<const short unsigned int, short unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const short unsigned int, short unsigned int>; T = std::pair<const short unsigned int, short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; reference = std::pair<const short unsigned int, short unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const short unsigned int, short unsigned int>; Value = std::pair<const short unsigned int, short unsigned int>; Key = short unsigned int; HashFcn = spp::spp_hash<short unsigned int>; ExtractKey = spp::sparse_hash_map<short unsigned int, short unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<short unsigned int, short unsigned int>::SetKey; EqualKey = std::equal_to<short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; reference = std::pair<const short unsigned int, short unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<short unsigned int, short unsigned int>::DefaultValue; KT = short unsigned int&; Value = std::pair<const short unsigned int, short unsigned int>; Key = short unsigned int; HashFcn = spp::spp_hash<short unsigned int>; ExtractKey = spp::sparse_hash_map<short unsigned int, short unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<short unsigned int, short unsigned int>::SetKey; EqualKey = std::equal_to<short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; value_type = std::pair<const short unsigned int, short unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = short unsigned int&; Key = short unsigned int; T = short unsigned int; HashFcn = spp::spp_hash<short unsigned int>; EqualKey = std::equal_to<short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> >; mapped_type = short unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:286:47: required from here
286 | eqclassHash[genesVec].second[readspmol] += 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const short unsigned int, short unsigned int>, spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> > >::value_type' {aka 'std::pair<const short unsigned int, short unsigned int>'} to 'spp::sparsegroup<std::pair<const short unsigned int, short unsigned int>, spp::libc_allocator<std::pair<const short unsigned int, short unsigned int> > >::mutable_reference' {aka 'std::pair<short unsigned int, short unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = short unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = short unsigned int; _T2 = short unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; mutable_value_type = std::pair<std::vector<unsigned int>, unsigned int>; reference = std::pair<const std::vector<unsigned int>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; pointer = std::pair<const std::vector<unsigned int>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::vector<unsigned int>, unsigned int>; T = std::pair<const std::vector<unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; reference = std::pair<const std::vector<unsigned int>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = boost::hash<std::vector<unsigned int> >; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, boost::hash<std::vector<unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, boost::hash<std::vector<unsigned int> > >::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; reference = std::pair<const std::vector<unsigned int>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, boost::hash<std::vector<unsigned int> > >::DefaultValue; KT = std::vector<unsigned int>&; Value = std::pair<const std::vector<unsigned int>, unsigned int>; Key = std::vector<unsigned int>; HashFcn = boost::hash<std::vector<unsigned int> >; ExtractKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, boost::hash<std::vector<unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::vector<unsigned int>, unsigned int, boost::hash<std::vector<unsigned int> > >::SetKey; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; value_type = std::pair<const std::vector<unsigned int>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::vector<unsigned int>&; Key = std::vector<unsigned int>; T = unsigned int; HashFcn = boost::hash<std::vector<unsigned int> >; EqualKey = std::equal_to<std::vector<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:413:29: required from here
413 | eqclassHash[genesVec] += 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >::value_type' {aka 'std::pair<const std::vector<unsigned int>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::vector<unsigned int>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector<unsigned int>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::vector<unsigned int>; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; mutable_value_type = std::pair<unsigned int, unsigned int>; reference = std::pair<const unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; pointer = std::pair<const unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; reference = std::pair<const unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, unsigned int>; Value = std::pair<const unsigned int, unsigned int>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; reference = std::pair<const unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, unsigned int>::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, unsigned int>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; value_type = std::pair<const unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:477:29: required from here
477 | vertexIndices[gene] = gid;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, unsigned int>, spp::libc_allocator<std::pair<const unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const unsigned int, unsigned int>, spp::libc_allocator<std::pair<const unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; value_type = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; reference = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; pointer = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from 'void spp::sparsetable<T, Alloc>::move(size_type, reference) [with T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int; reference = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>&]'
2251 | which_group(i).set(_alloc, pos_in_group(i), val);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from 'void spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_move_from(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
2830 | table.move(bucknum, *it); // moves the value to here
| ~~~~~~~~~~^~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
2948 | _move_from(mover, ht, min_buckets_wanted);
| ^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2680:30: required from 'bool spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_maybe_shrink() [with Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >]'
2680 | sparse_hashtable tmp(MoveDontCopy, *this, sz);
| ^~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from 'void spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::resize(size_type) [with Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
2846 | _maybe_shrink();
| ^~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3799:51: required from 'void spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::resize(size_type) [with Key = std::pair<unsigned int, unsigned int>; T = unsigned int; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
3799 | void resize(size_type cnt) { rep.resize(cnt); }
| ~~~~~~~~~~^~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3801:41: required from 'void spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::reserve(size_type) [with Key = std::pair<unsigned int, unsigned int>; T = unsigned int; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
3801 | void reserve(size_type cnt) { resize(cnt); } // c++11
| ^~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:39:25: required from here
39 | vertexIndexMap.reserve(numClasses);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> > >::value_type' {aka 'std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::pair<unsigned int, unsigned int>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair<unsigned int, unsigned int>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::pair<unsigned int, unsigned int>; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:65:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h: In instantiation of 'T* spp::libc_allocator<T>::reallocate(pointer, size_t) [with T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; pointer = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>*; size_t = long unsigned int]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1383:38: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1383 | _group = alloc.reallocate(_group, num_alloc);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; pointer = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from 'void spp::sparsetable<T, Alloc>::move(size_type, reference) [with T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int; reference = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>&]'
2251 | which_group(i).set(_alloc, pos_in_group(i), val);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from 'void spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_move_from(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
2830 | table.move(bucknum, *it); // moves the value to here
| ~~~~~~~~~~^~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
2948 | _move_from(mover, ht, min_buckets_wanted);
| ^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2680:30: required from 'bool spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_maybe_shrink() [with Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >]'
2680 | sparse_hashtable tmp(MoveDontCopy, *this, sz);
| ^~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from 'void spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::resize(size_type) [with Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
2846 | _maybe_shrink();
| ^~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3799:51: required from 'void spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::resize(size_type) [with Key = std::pair<unsigned int, unsigned int>; T = unsigned int; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
3799 | void resize(size_type cnt) { rep.resize(cnt); }
| ~~~~~~~~~~^~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3801:41: required from 'void spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::reserve(size_type) [with Key = std::pair<unsigned int, unsigned int>; T = unsigned int; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
3801 | void reserve(size_type cnt) { resize(cnt); } // c++11
| ^~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:39:25: required from here
39 | vertexIndexMap.reserve(numClasses);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h:425:51: warning: 'void* realloc(void*, size_t)' moving an object of non-trivially copyable type 'struct std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>'; use 'new' and 'delete' instead [-Wclass-memaccess]
425 | pointer res = static_cast<pointer>(realloc(p, new_size * sizeof(T)));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_algobase.h:64,
from /usr/include/c++/14/string:51,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/streambuf:43,
from /usr/include/c++/14/bits/streambuf_iterator.h:35,
from /usr/include/c++/14/iterator:66,
from /usr/include/boost/graph/graph_traits.hpp:14,
from /usr/include/boost/graph/depth_first_search.hpp:17,
from /usr/include/boost/graph/connected_components.hpp:15,
from /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:4:
/usr/include/c++/14/bits/stl_pair.h:284:12: note: 'struct std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>' declared here
284 | struct pair
| ^~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; mutable_value_type = std::pair<std::pair<unsigned int, unsigned int>, unsigned int>; reference = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; pointer = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from 'void spp::sparsetable<T, Alloc>::move(size_type, reference) [with T = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int; reference = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>&]'
2251 | which_group(i).set(_alloc, pos_in_group(i), val);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from 'void spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_move_from(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
2830 | table.move(bucknum, *it); // moves the value to here
| ~~~~~~~~~~^~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>&, size_type) [with Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
2948 | _move_from(mover, ht, min_buckets_wanted);
| ^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2680:30: required from 'bool spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_maybe_shrink() [with Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >]'
2680 | sparse_hashtable tmp(MoveDontCopy, *this, sz);
| ^~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from 'void spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::resize(size_type) [with Value = std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>; Key = std::pair<unsigned int, unsigned int>; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; ExtractKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SelectKey; SetKey = spp::sparse_hash_map<std::pair<unsigned int, unsigned int>, unsigned int, boost::hash<std::pair<unsigned int, unsigned int> > >::SetKey; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
2846 | _maybe_shrink();
| ^~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3799:51: required from 'void spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::resize(size_type) [with Key = std::pair<unsigned int, unsigned int>; T = unsigned int; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
3799 | void resize(size_type cnt) { rep.resize(cnt); }
| ~~~~~~~~~~^~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3801:41: required from 'void spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::reserve(size_type) [with Key = std::pair<unsigned int, unsigned int>; T = unsigned int; HashFcn = boost::hash<std::pair<unsigned int, unsigned int> >; EqualKey = std::equal_to<std::pair<unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> >; size_type = long unsigned int]'
3801 | void reserve(size_type cnt) { resize(cnt); } // c++11
| ^~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp:39:25: required from here
39 | vertexIndexMap.reserve(numClasses);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> > >::value_type' {aka 'std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::pair<unsigned int, unsigned int>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::pair<unsigned int, unsigned int>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair<unsigned int, unsigned int>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::pair<unsigned int, unsigned int>; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; pointer = std::pair<const std::__cxx11::basic_string<char>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string<char>&; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::__cxx11::basic_string<char>&; Key = std::__cxx11::basic_string<char>; T = unsigned int; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:12:31: required from here
12 | txpIdxMap[ transcripts[i] ] = i;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::value_type' {aka 'std::pair<const std::__cxx11::basic_string<char>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::__cxx11::basic_string<char>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string<char>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::__cxx11::basic_string<char>; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; value_type = std::pair<const unsigned int, unsigned int>; reference = std::pair<const unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; pointer = std::pair<const unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; reference = std::pair<const unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, unsigned int>; Value = std::pair<const unsigned int, unsigned int>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; reference = std::pair<const unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, unsigned int>::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, unsigned int>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; value_type = std::pair<const unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:35:23: required from here
35 | txpToGeneMap[tid] = gid;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, unsigned int>, spp::libc_allocator<std::pair<const unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const unsigned int, unsigned int>, spp::libc_allocator<std::pair<const unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; value_type = std::pair<const long unsigned int, long unsigned int>; reference = std::pair<const long unsigned int, long unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, long unsigned int>; T = std::pair<const long unsigned int, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, long unsigned int>; T = std::pair<const long unsigned int, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; pointer = std::pair<const long unsigned int, long unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, long unsigned int>; T = std::pair<const long unsigned int, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; reference = std::pair<const long unsigned int, long unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, long unsigned int>; Value = std::pair<const long unsigned int, long unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, long unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; reference = std::pair<const long unsigned int, long unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, long unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, long unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, long unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; value_type = std::pair<const long unsigned int, long unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; mapped_type = long unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:98:21: required from here
98 | barcodeMap[i] = i;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, long unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, long unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, long unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, long unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = long unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; reference = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; pointer = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Value = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, long unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::__cxx11::basic_string<char>, long unsigned int>::DefaultValue; KT = const std::__cxx11::basic_string<char>&; Value = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, long unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = const std::__cxx11::basic_string<char>&; Key = std::__cxx11::basic_string<char>; T = long unsigned int; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; mapped_type = long unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:105:26: required from here
105 | trueBarcodeMap[bc] = idx;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, long unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> > >::value_type' {aka 'std::pair<const std::__cxx11::basic_string<char>, long unsigned int>'} to 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, long unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> > >::mutable_reference' {aka 'std::pair<std::__cxx11::basic_string<char>, long unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string<char>; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::__cxx11::basic_string<char>; _T2 = long unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mutable_value_type = std::pair<long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; mutable_value_type = std::pair<std::__cxx11::basic_string<char>, unsigned int>; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; pointer = std::pair<const std::__cxx11::basic_string<char>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string<char>&; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::__cxx11::basic_string<char>&; Key = std::__cxx11::basic_string<char>; T = unsigned int; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:12:31: required from here
12 | txpIdxMap[ transcripts[i] ] = i;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::value_type' {aka 'std::pair<const std::__cxx11::basic_string<char>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::__cxx11::basic_string<char>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string<char>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::__cxx11::basic_string<char>; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; mutable_value_type = std::pair<unsigned int, unsigned int>; reference = std::pair<const unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; pointer = std::pair<const unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, unsigned int>; T = std::pair<const unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; reference = std::pair<const unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, unsigned int>; Value = std::pair<const unsigned int, unsigned int>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; reference = std::pair<const unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, unsigned int>::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, unsigned int>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; value_type = std::pair<const unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:35:23: required from here
35 | txpToGeneMap[tid] = gid;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, unsigned int>, spp::libc_allocator<std::pair<const unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const unsigned int, unsigned int>, spp::libc_allocator<std::pair<const unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; mutable_value_type = std::pair<long unsigned int, long unsigned int>; reference = std::pair<const long unsigned int, long unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const long unsigned int, long unsigned int>; T = std::pair<const long unsigned int, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, long unsigned int>; T = std::pair<const long unsigned int, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, long unsigned int>; T = std::pair<const long unsigned int, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; pointer = std::pair<const long unsigned int, long unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, long unsigned int>; T = std::pair<const long unsigned int, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; reference = std::pair<const long unsigned int, long unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, long unsigned int>; Value = std::pair<const long unsigned int, long unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, long unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; reference = std::pair<const long unsigned int, long unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, long unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, long unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, long unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; value_type = std::pair<const long unsigned int, long unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> >; mapped_type = long unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:98:21: required from here
98 | barcodeMap[i] = i;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, long unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, long unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, long unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, long unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, long unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = long unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; mutable_value_type = std::pair<std::__cxx11::basic_string<char>, long unsigned int>; reference = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; pointer = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Value = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, long unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::__cxx11::basic_string<char>, long unsigned int>::DefaultValue; KT = const std::__cxx11::basic_string<char>&; Value = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, long unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, long unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = const std::__cxx11::basic_string<char>&; Key = std::__cxx11::basic_string<char>; T = long unsigned int; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> >; mapped_type = long unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp:105:26: required from here
105 | trueBarcodeMap[bc] = idx;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, long unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> > >::value_type' {aka 'std::pair<const std::__cxx11::basic_string<char>, long unsigned int>'} to 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, long unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> > >::mutable_reference' {aka 'std::pair<std::__cxx11::basic_string<char>, long unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string<char>; _U2 = long unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::__cxx11::basic_string<char>; _T2 = long unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::DropSeq; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::DropSeq; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
938 | processBarcodes(barcodeFiles,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
939 | readFiles,
| ~~~~~~~~~~
940 | aopt,
| ~~~~~
941 | barcodeSoftMap,
| ~~~~~~~~~~~~~~~
942 | trueBarcodes,
| ~~~~~~~~~~~~~
943 | freqCounter,
| ~~~~~~~~~~~~
944 | numLowConfidentBarcode);
| ~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1084:23: required from here
1084 | initiatePipeline(aopt, sopt, orderedOptions,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1085 | vm, commentString, noTgMap,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
1086 | barcodeFiles, readFiles, salmonIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::InDropV2; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::InDropV2; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::InDropV2; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
938 | processBarcodes(barcodeFiles,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
939 | readFiles,
| ~~~~~~~~~~
940 | aopt,
| ~~~~~
941 | barcodeSoftMap,
| ~~~~~~~~~~~~~~~
942 | trueBarcodes,
| ~~~~~~~~~~~~~
943 | freqCounter,
| ~~~~~~~~~~~~
944 | numLowConfidentBarcode);
| ~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1094:25: required from here
1094 | initiatePipeline(aopt, sopt, orderedOptions,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1095 | vm, commentString, noTgMap,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
1096 | barcodeFiles, readFiles, salmonIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CITESeq; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CITESeq; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CITESeq; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
938 | processBarcodes(barcodeFiles,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
939 | readFiles,
| ~~~~~~~~~~
940 | aopt,
| ~~~~~
941 | barcodeSoftMap,
| ~~~~~~~~~~~~~~~
942 | trueBarcodes,
| ~~~~~~~~~~~~~
943 | freqCounter,
| ~~~~~~~~~~~~
944 | numLowConfidentBarcode);
| ~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1110:25: required from here
1110 | initiatePipeline(aopt, sopt, orderedOptions,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1111 | vm, commentString, noTgMap,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
1112 | barcodeFiles, readFiles, salmonIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::ChromiumV3; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::ChromiumV3; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::ChromiumV3; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
938 | processBarcodes(barcodeFiles,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
939 | readFiles,
| ~~~~~~~~~~
940 | aopt,
| ~~~~~
941 | barcodeSoftMap,
| ~~~~~~~~~~~~~~~
942 | trueBarcodes,
| ~~~~~~~~~~~~~
943 | freqCounter,
| ~~~~~~~~~~~~
944 | numLowConfidentBarcode);
| ~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1122:23: required from here
1122 | initiatePipeline(aopt, sopt, orderedOptions,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1123 | vm, commentString, noTgMap,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
1124 | barcodeFiles, readFiles, salmonIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Chromium; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Chromium; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Chromium; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
938 | processBarcodes(barcodeFiles,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
939 | readFiles,
| ~~~~~~~~~~
940 | aopt,
| ~~~~~
941 | barcodeSoftMap,
| ~~~~~~~~~~~~~~~
942 | trueBarcodes,
| ~~~~~~~~~~~~~
943 | freqCounter,
| ~~~~~~~~~~~~
944 | numLowConfidentBarcode);
| ~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1129:23: required from here
1129 | initiatePipeline(aopt, sopt, orderedOptions,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1130 | vm, commentString, noTgMap,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
1131 | barcodeFiles, readFiles, salmonIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Gemcode; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Gemcode; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Gemcode; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
938 | processBarcodes(barcodeFiles,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
939 | readFiles,
| ~~~~~~~~~~
940 | aopt,
| ~~~~~
941 | barcodeSoftMap,
| ~~~~~~~~~~~~~~~
942 | trueBarcodes,
| ~~~~~~~~~~~~~
943 | freqCounter,
| ~~~~~~~~~~~~
944 | numLowConfidentBarcode);
| ~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1136:23: required from here
1136 | initiatePipeline(aopt, sopt, orderedOptions,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1137 | vm, commentString, noTgMap,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
1138 | unmateFiles, readFiles, salmonIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CELSeq; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CELSeq; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CELSeq; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
938 | processBarcodes(barcodeFiles,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
939 | readFiles,
| ~~~~~~~~~~
940 | aopt,
| ~~~~~
941 | barcodeSoftMap,
| ~~~~~~~~~~~~~~~
942 | trueBarcodes,
| ~~~~~~~~~~~~~
943 | freqCounter,
| ~~~~~~~~~~~~
944 | numLowConfidentBarcode);
| ~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1143:23: required from here
1143 | initiatePipeline(aopt, sopt, orderedOptions,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1144 | vm, commentString, noTgMap,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
1145 | barcodeFiles, readFiles, salmonIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CELSeq2; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CELSeq2; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CELSeq2; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
938 | processBarcodes(barcodeFiles,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
939 | readFiles,
| ~~~~~~~~~~
940 | aopt,
| ~~~~~
941 | barcodeSoftMap,
| ~~~~~~~~~~~~~~~
942 | trueBarcodes,
| ~~~~~~~~~~~~~
943 | freqCounter,
| ~~~~~~~~~~~~
944 | numLowConfidentBarcode);
| ~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1150:23: required from here
1150 | initiatePipeline(aopt, sopt, orderedOptions,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1151 | vm, commentString, noTgMap,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
1152 | barcodeFiles, readFiles, salmonIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SplitSeqV1; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SplitSeqV1; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SplitSeqV1; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
938 | processBarcodes(barcodeFiles,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
939 | readFiles,
| ~~~~~~~~~~
940 | aopt,
| ~~~~~
941 | barcodeSoftMap,
| ~~~~~~~~~~~~~~~
942 | trueBarcodes,
| ~~~~~~~~~~~~~
943 | freqCounter,
| ~~~~~~~~~~~~
944 | numLowConfidentBarcode);
| ~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1157:23: required from here
1157 | initiatePipeline(aopt, sopt, orderedOptions,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1158 | vm, commentString, noTgMap,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
1159 | barcodeFiles, readFiles, salmonIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SplitSeqV2; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SplitSeqV2; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SplitSeqV2; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
938 | processBarcodes(barcodeFiles,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
939 | readFiles,
| ~~~~~~~~~~
940 | aopt,
| ~~~~~
941 | barcodeSoftMap,
| ~~~~~~~~~~~~~~~
942 | trueBarcodes,
| ~~~~~~~~~~~~~
943 | freqCounter,
| ~~~~~~~~~~~~
944 | numLowConfidentBarcode);
| ~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1164:23: required from here
1164 | initiatePipeline(aopt, sopt, orderedOptions,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1165 | vm, commentString, noTgMap,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
1166 | barcodeFiles, readFiles, salmonIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::QuartzSeq2; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::QuartzSeq2; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::QuartzSeq2; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
938 | processBarcodes(barcodeFiles,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
939 | readFiles,
| ~~~~~~~~~~
940 | aopt,
| ~~~~~
941 | barcodeSoftMap,
| ~~~~~~~~~~~~~~~
942 | trueBarcodes,
| ~~~~~~~~~~~~~
943 | freqCounter,
| ~~~~~~~~~~~~
944 | numLowConfidentBarcode);
| ~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1171:23: required from here
1171 | initiatePipeline(aopt, sopt, orderedOptions,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1172 | vm, commentString, noTgMap,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
1173 | barcodeFiles, readFiles, salmonIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SciSeq3; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SciSeq3; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SciSeq3; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
938 | processBarcodes(barcodeFiles,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
939 | readFiles,
| ~~~~~~~~~~
940 | aopt,
| ~~~~~
941 | barcodeSoftMap,
| ~~~~~~~~~~~~~~~
942 | trueBarcodes,
| ~~~~~~~~~~~~~
943 | freqCounter,
| ~~~~~~~~~~~~
944 | numLowConfidentBarcode);
| ~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1177:23: required from here
1177 | initiatePipeline(aopt, sopt, orderedOptions,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1178 | vm, commentString, noTgMap,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
1179 | barcodeFiles, readFiles, salmonIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Custom; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Custom; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Custom; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
938 | processBarcodes(barcodeFiles,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
939 | readFiles,
| ~~~~~~~~~~
940 | aopt,
| ~~~~~
941 | barcodeSoftMap,
| ~~~~~~~~~~~~~~~
942 | trueBarcodes,
| ~~~~~~~~~~~~~
943 | freqCounter,
| ~~~~~~~~~~~~
944 | numLowConfidentBarcode);
| ~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1183:23: required from here
1183 | initiatePipeline(aopt, sopt, orderedOptions,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1184 | vm, commentString, noTgMap,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
1185 | barcodeFiles, readFiles, salmonIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18,
from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadExperiment.hpp:7:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CustomGeometry; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CustomGeometry; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
780 | indexBarcodes(aopt, freqCounter, trueBarcodes, barcodeSoftMap);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20: required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CustomGeometry; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
938 | processBarcodes(barcodeFiles,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
939 | readFiles,
| ~~~~~~~~~~
940 | aopt,
| ~~~~~
941 | barcodeSoftMap,
| ~~~~~~~~~~~~~~~
942 | trueBarcodes,
| ~~~~~~~~~~~~~
943 | freqCounter,
| ~~~~~~~~~~~~
944 | numLowConfidentBarcode);
| ~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1189:23: required from here
1189 | initiatePipeline(aopt, sopt, orderedOptions,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1190 | vm, commentString, noTgMap,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
1191 | barcodeFiles, readFiles, salmonIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
488 | for (const auto trueBarcode: trueBarcodes){
| ^~~~~~~~~~~
| &
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const short unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; value_type = std::pair<const short unsigned int, unsigned int>; reference = std::pair<const short unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const short unsigned int, unsigned int>; T = std::pair<const short unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const short unsigned int, unsigned int>; T = std::pair<const short unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; pointer = std::pair<const short unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const short unsigned int, unsigned int>; T = std::pair<const short unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; reference = std::pair<const short unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const short unsigned int, unsigned int>; Value = std::pair<const short unsigned int, unsigned int>; Key = short unsigned int; HashFcn = spp::spp_hash<short unsigned int>; ExtractKey = spp::sparse_hash_map<short unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<short unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; reference = std::pair<const short unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<short unsigned int, unsigned int>::DefaultValue; KT = const short unsigned int&; Value = std::pair<const short unsigned int, unsigned int>; Key = short unsigned int; HashFcn = spp::spp_hash<short unsigned int>; ExtractKey = spp::sparse_hash_map<short unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<short unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; value_type = std::pair<const short unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = const short unsigned int&; Key = short unsigned int; T = unsigned int; HashFcn = spp::spp_hash<short unsigned int>; EqualKey = std::equal_to<short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:747:45: required from here
747 | arboFragCounts[gid][it.first] += it.second;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const short unsigned int, unsigned int>, spp::libc_allocator<std::pair<const short unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const short unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const short unsigned int, unsigned int>, spp::libc_allocator<std::pair<const short unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<short unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = short unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mutable_value_type = std::pair<long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::DropSeq; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::DropSeq>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::DropSeq>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::DropSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2777:62: required from here
2777 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::DropSeq; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::DropSeq>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::DropSeq>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::DropSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2777:62: required from here
2777 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const short unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; mutable_value_type = std::pair<short unsigned int, unsigned int>; reference = std::pair<const short unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const short unsigned int, unsigned int>; T = std::pair<const short unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const short unsigned int, unsigned int>; T = std::pair<const short unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const short unsigned int, unsigned int>; T = std::pair<const short unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; pointer = std::pair<const short unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const short unsigned int, unsigned int>; T = std::pair<const short unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; reference = std::pair<const short unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const short unsigned int, unsigned int>; Value = std::pair<const short unsigned int, unsigned int>; Key = short unsigned int; HashFcn = spp::spp_hash<short unsigned int>; ExtractKey = spp::sparse_hash_map<short unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<short unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; reference = std::pair<const short unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<short unsigned int, unsigned int>::DefaultValue; KT = const short unsigned int&; Value = std::pair<const short unsigned int, unsigned int>; Key = short unsigned int; HashFcn = spp::spp_hash<short unsigned int>; ExtractKey = spp::sparse_hash_map<short unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<short unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; value_type = std::pair<const short unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = const short unsigned int&; Key = short unsigned int; T = unsigned int; HashFcn = spp::spp_hash<short unsigned int>; EqualKey = std::equal_to<short unsigned int>; Alloc = spp::libc_allocator<std::pair<const short unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:747:45: required from here
747 | arboFragCounts[gid][it.first] += it.second;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const short unsigned int, unsigned int>, spp::libc_allocator<std::pair<const short unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const short unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const short unsigned int, unsigned int>, spp::libc_allocator<std::pair<const short unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<short unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const short unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = short unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; pointer = std::pair<const std::__cxx11::basic_string<char>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string<char>&; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::__cxx11::basic_string<char>&; Key = std::__cxx11::basic_string<char>; T = unsigned int; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1087:29: required from 'bool CollapsedCellOptimizer::optimize(EqMapT&, spp::sparse_hash_map<unsigned int, unsigned int>&, spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>&, AlevinOpts<ProtocolT>&, GZipWriter&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<unsigned int>&, CFreqMapT&, size_t) [with ProtocolT = alevin::protocols::DropSeq; EqMapT = libcuckoo::cuckoohash_map<TranscriptGroup, SCTGValue, TranscriptGroupHasher, std::equal_to<TranscriptGroup>, std::allocator<std::pair<const TranscriptGroup, SCTGValue> >, 4>; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
1087 | mRnaGenes.insert(geneIdxMap[ gene ]);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1426:68: required from here
1426 | size_t numLowConfidentBarcode);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::value_type' {aka 'std::pair<const std::__cxx11::basic_string<char>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::__cxx11::basic_string<char>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string<char>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::__cxx11::basic_string<char>; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CITESeq; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::CITESeq>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::CITESeq>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CITESeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2791:62: required from here
2791 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CITESeq; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::CITESeq>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::CITESeq>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CITESeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2791:62: required from here
2791 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; mutable_value_type = std::pair<std::__cxx11::basic_string<char>, unsigned int>; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; pointer = std::pair<const std::__cxx11::basic_string<char>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string<char>&; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::__cxx11::basic_string<char>&; Key = std::__cxx11::basic_string<char>; T = unsigned int; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1087:29: required from 'bool CollapsedCellOptimizer::optimize(EqMapT&, spp::sparse_hash_map<unsigned int, unsigned int>&, spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>&, AlevinOpts<ProtocolT>&, GZipWriter&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<unsigned int>&, CFreqMapT&, size_t) [with ProtocolT = alevin::protocols::DropSeq; EqMapT = libcuckoo::cuckoohash_map<TranscriptGroup, SCTGValue, TranscriptGroupHasher, std::equal_to<TranscriptGroup>, std::allocator<std::pair<const TranscriptGroup, SCTGValue> >, 4>; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
1087 | mRnaGenes.insert(geneIdxMap[ gene ]);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedCellOptimizer.cpp:1426:68: required from here
1426 | size_t numLowConfidentBarcode);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::value_type' {aka 'std::pair<const std::__cxx11::basic_string<char>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::__cxx11::basic_string<char>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string<char>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::__cxx11::basic_string<char>; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::InDropV2; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::InDropV2>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::InDropV2>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDropV2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDropV2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::InDropV2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2804:58: required from here
2804 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::InDropV2; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::InDropV2>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::InDropV2>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDropV2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDropV2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::InDropV2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2804:58: required from here
2804 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12,
from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192,
from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/Util.hpp:19,
from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadPair.hpp:6,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentGroup.hpp:15,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:12,
from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantifyAlignments.cpp:33:
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
197 | registry_t<Mutex>() {}
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
198 | registry_t<Mutex>(const registry_t<Mutex>&) = delete;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >'
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::ChromiumV3; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::ChromiumV3>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::ChromiumV3>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::ChromiumV3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2817:58: required from here
2817 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::ChromiumV3; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::ChromiumV3>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::ChromiumV3>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::ChromiumV3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2817:58: required from here
2817 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18,
from /build/reproducible-path/salmon-1.10.2+ds1/include/ReadExperiment.hpp:7,
from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonMappingUtils.hpp:44,
from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantify.cpp:93:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Chromium; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::Chromium>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::Chromium>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Chromium; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2830:58: required from here
2830 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Chromium; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::Chromium>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::Chromium>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Chromium; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2830:58: required from here
2830 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Gemcode; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::Gemcode>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::Gemcode>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Gemcode; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2843:58: required from here
2843 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Gemcode; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::Gemcode>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::Gemcode>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Gemcode; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2843:58: required from here
2843 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CELSeq; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::CELSeq>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::CELSeq>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CELSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2856:58: required from here
2856 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CELSeq; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::CELSeq>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::CELSeq>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CELSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2856:58: required from here
2856 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CELSeq2; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::CELSeq2>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::CELSeq2>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CELSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2869:58: required from here
2869 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mutable_value_type = std::pair<long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CELSeq2; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::CELSeq2>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::CELSeq2>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CELSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2869:58: required from here
2869 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SplitSeqV1; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::SplitSeqV1>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::SplitSeqV1>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV1; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV1; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SplitSeqV1; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2882:58: required from here
2882 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::SplitSeqV1; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::SplitSeqV1>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::SplitSeqV1>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV1; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV1; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SplitSeqV1; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2882:58: required from here
2882 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SplitSeqV2; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::SplitSeqV2>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::SplitSeqV2>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SplitSeqV2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2895:58: required from here
2895 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::SplitSeqV2; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::SplitSeqV2>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::SplitSeqV2>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SplitSeqV2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2895:58: required from here
2895 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mutable_value_type = std::pair<long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::QuartzSeq2; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::QuartzSeq2>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::QuartzSeq2>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::QuartzSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2908:58: required from here
2908 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::QuartzSeq2; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::QuartzSeq2>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::QuartzSeq2>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::QuartzSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2908:58: required from here
2908 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SciSeq3; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::SciSeq3>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::SciSeq3>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SciSeq3; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SciSeq3; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SciSeq3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2923:62: required from here
2923 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::SciSeq3; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::SciSeq3>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::SciSeq3>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SciSeq3; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SciSeq3; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SciSeq3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2923:62: required from here
2923 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Custom; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::Custom>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::Custom>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Custom; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2940:58: required from here
2940 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Custom; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::Custom>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::Custom>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Custom; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2940:58: required from here
2940 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CustomGeometry; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::CustomGeometry>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::CustomGeometry>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1751 | processFunctor(i, pairedParserPtr.get(), sidx->puffSparseIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CustomGeometry; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2954:58: required from here
2954 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CustomGeometry; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::CustomGeometry>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::CustomGeometry>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishIndex; size_t = long unsigned int]'
1730 | process_reads_sc_sketch(
| ~~~~~~~~~~~~~~~~~~~~~~~^
1731 | parserPtr, readExp, rl, structureVec[i], numObservedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1732 | numAssignedFragments, numUniqueMappings, numValidHits, smallSeqs, nSeqs, index,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1733 | transcripts, fragLengthDist, salmonOpts, num_chunks, rad_file, unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1734 | fileMutex, unmapped_bc_mutex, ioMutex, alevinOpts, mstats
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1735 | );
| ~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1753:23: required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
1753 | processFunctor(i, pairedParserPtr.get(), sidx->puffIndex());
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2094:32: required from 'bool do_sc_align(ReadExperimentT&, SalmonOpts&, MappingStatistics&, uint32_t, AlevinOpts<ProtocolT>&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; uint32_t = unsigned int]'
2094 | sc_align_read_library<AlnT>(experiment, rl, sidx, transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2095 | numObservedFragments, numAssignedFragments,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2096 | smallSeqs, nSeqs, burnedIn,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2097 | fragLengthDist, salmonOpts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
2098 | num_chunks,
| ~~~~~~~~~~~
2099 | rad_file,
| ~~~~~~~~~
2100 | unmapped_bc_file,
| ~~~~~~~~~~~~~~~~~
2101 | fileMutex,
| ~~~~~~~~~~
2102 | unmapped_bc_mutex,
| ~~~~~~~~~~~~~~~~~~
2103 | ioMutex, numQuantThreads, groupVec,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2104 | alevinOpts, mstats);
| ~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2521:50: required from 'int alevin_sc_align(AlevinOpts<ProtocolT>&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CustomGeometry; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>]'
2521 | bool mapping_ok = do_sc_align<QuasiAlignment>(experiment, sopt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
2522 | mstats, sopt.numThreads, aopt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2954:58: required from here
2954 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:489:19: warning: variable 'expectedLibraryFormat' set but not used [-Wunused-but-set-variable]
489 | LibraryFormat expectedLibraryFormat = rl.format();
| ^~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
397 | IndexT* qidx, std::vector<Transcript>& transcripts,
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinHash.hpp:10,
from /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:58:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mutable_value_type = std::pair<long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47,
from /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:95:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mutable_value_type = std::pair<long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; pointer = std::pair<const std::__cxx11::basic_string<char>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string<char>&; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::__cxx11::basic_string<char>&; Key = std::__cxx11::basic_string<char>; T = unsigned int; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2647:50: required from 'int alevinQuant(AlevinOpts<ProtocolT>&, SalmonOpts&, SoftMapT&, TrueBcsT&, spp::sparse_hash_map<unsigned int, unsigned int>&, spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>&, boost::program_options::parsed_options&, CFreqMapT&, size_t, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
2647 | trueBarcodesIndexMap[ trueBarcodesVec[i] ] = i;
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2786:54: required from here
2786 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::value_type' {aka 'std::pair<const std::__cxx11::basic_string<char>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::__cxx11::basic_string<char>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string<char>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::__cxx11::basic_string<char>; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; mutable_value_type = std::pair<std::__cxx11::basic_string<char>, unsigned int>; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; pointer = std::pair<const std::__cxx11::basic_string<char>, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; reference = std::pair<const std::__cxx11::basic_string<char>, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string<char>&; Value = std::pair<const std::__cxx11::basic_string<char>, unsigned int>; Key = std::__cxx11::basic_string<char>; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; ExtractKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>::SetKey; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; value_type = std::pair<const std::__cxx11::basic_string<char>, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = std::__cxx11::basic_string<char>&; Key = std::__cxx11::basic_string<char>; T = unsigned int; HashFcn = spp::spp_hash<std::__cxx11::basic_string<char> >; EqualKey = std::equal_to<std::__cxx11::basic_string<char> >; Alloc = spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2647:50: required from 'int alevinQuant(AlevinOpts<ProtocolT>&, SalmonOpts&, SoftMapT&, TrueBcsT&, spp::sparse_hash_map<unsigned int, unsigned int>&, spp::sparse_hash_map<std::__cxx11::basic_string<char>, unsigned int>&, boost::program_options::parsed_options&, CFreqMapT&, size_t, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; boost::program_options::parsed_options = boost::program_options::basic_parsed_options<char>; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
2647 | trueBarcodesIndexMap[ trueBarcodesVec[i] ] = i;
/build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2786:54: required from here
2786 | std::unique_ptr<SalmonIndex>& salmonIndex);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::value_type' {aka 'std::pair<const std::__cxx11::basic_string<char>, unsigned int>'} to 'spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, unsigned int> > >::mutable_reference' {aka 'std::pair<std::__cxx11::basic_string<char>, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string<char>; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = std::__cxx11::basic_string<char>; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18,
from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19:
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_set_val(value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1440 | _set_val(&_group[offset], val);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1355 | *(mutable_pointer)p = std::move((mutable_reference)val);
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map<long unsigned int, unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > >; mapped_type = spp::sparse_hash_map<long unsigned int, unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:25: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_map<long unsigned int, unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map<long unsigned int, unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map<long unsigned int, unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mutable_value_type = std::pair<long unsigned int, unsigned int>; reference = std::pair<const long unsigned int, unsigned int>&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant<bool, true>]'
1390 | _init_val((mutable_pointer)(_group + offset), val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; pointer = std::pair<const long unsigned int, unsigned int>*; allocator_type = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const long unsigned int, unsigned int>; T = std::pair<const long unsigned int, unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const long unsigned int, unsigned int>; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; reference = std::pair<const long unsigned int, unsigned int>&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<long unsigned int, unsigned int>::DefaultValue; KT = long unsigned int&; Value = std::pair<const long unsigned int, unsigned int>; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, unsigned int>::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; value_type = std::pair<const long unsigned int, unsigned int>]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash<long unsigned int>; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, unsigned int> >; mapped_type = unsigned int]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:51:30: required from here
51 | barcodeGroup[barcode][umi] = 1;
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::value_type' {aka 'std::pair<const long unsigned int, unsigned int>'} to 'spp::sparsegroup<std::pair<const long unsigned int, unsigned int>, spp::libc_allocator<std::pair<const long unsigned int, unsigned int> > >::mutable_reference' {aka 'std::pair<long unsigned int, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = unsigned int; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = long unsigned int; _T2 = unsigned int]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup<T, Alloc>::_init_val(mutable_value_type*, reference) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mutable_value_type = std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&]':
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup<T, Alloc>::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant<bool, false>]'
1407 | _init_val((mutable_pointer)&_group[num_items], val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup<T, Alloc>::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1435 | _set_aux(alloc, offset, val, check_alloc_type());
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup<T, Alloc>::value_type* spp::sparsegroup<T, Alloc>::set(allocator_type&, size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; pointer = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >*; allocator_type = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; size_type = unsigned char]'
1453 | _set(alloc, i, offset, val); // may change _group pointer
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:2242:28: required from 'spp::sparsetable<T, Alloc>::value_type& spp::sparsetable<T, Alloc>::set(size_type, Val&) [with Val = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
2242 | pointer p(group.set(_alloc, pos_in_group(i), val));
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3170:25: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_insert_at(T&, size_type, bool) [with T = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; reference = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >&; size_type = long unsigned int]'
3170 | return table.set(pos, obj);
| ~~~~~~~~~^~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3287:38: required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::value_type& spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::DefaultValue; KT = unsigned int&; Value = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, spp::sparse_hash_set<unsigned int> >::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; value_type = std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >]'
3287 | return _insert_at(def, erased ? erased_pos : bucknum, erased);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:3813:57: required from 'spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::mapped_type& spp::sparse_hash_map<Key, T, HashFcn, EqualKey, Alloc>::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set<unsigned int>; HashFcn = spp::spp_hash<unsigned int>; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > >; mapped_type = spp::sparse_hash_set<unsigned int>]'
3813 | return rep.template find_or_insert<DefaultValue>(std::forward<KT>(key)).second;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:28:21: required from here
28 | edges[source].insert(sink);
| ^
/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::value_type' {aka 'std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >'} to 'spp::sparsegroup<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> >, spp::libc_allocator<std::pair<const unsigned int, spp::sparse_hash_set<unsigned int> > > >::mutable_reference' {aka 'std::pair<unsigned int, spp::sparse_hash_set<unsigned int> >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set<unsigned int>; typename std::enable_if<(std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ConstructiblePair<_U1, _U2>() && std::_PCC<((! std::is_same<_T1, _U1>::value) || (! std::is_same<_T2, _U2>::value)), _T1, _T2>::_ImplicitlyConvertiblePair<_U1, _U2>()), bool>::type <anonymous> = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set<unsigned int>]' [-Wcast-user-defined]
1339 | ::new (p) value_type(std::move((mutable_reference)val));
| ^~~~~~~~~~~~~~~~~~~~~~
[100%] Linking CXX executable salmon
cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/salmon.dir/link.d CMakeFiles/salmon.dir/EMUtils.cpp.o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o CMakeFiles/salmon.dir/Salmon.cpp.o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o CMakeFiles/salmon.dir/Graph.cpp.o CMakeFiles/salmon.dir/DedupUMI.cpp.o CMakeFiles/salmon.dir/Alevin.cpp.o CMakeFiles/salmon.dir/AlevinHash.cpp.o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o CMakeFiles/salmon.dir/WhiteList.cpp.o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o CMakeFiles/salmon.dir/GZipWriter.cpp.o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o CMakeFiles/salmon.dir/FASTAParser.cpp.o CMakeFiles/salmon.dir/AlignmentModel.cpp.o CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o CMakeFiles/salmon.dir/AlignmentCommon.cpp.o CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o CMakeFiles/salmon.dir/BAMUtils.cpp.o -o salmon -L/build/reproducible-path/salmon-1.10.2+ds1/lib -L/build/reproducible-path/salmon-1.10.2+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" ../external/pufferfish/src/libpuffer.a libsalmon_core.a ../external/pufferfish/external/twopaco/graphconstructor/libtwopaco.a ../external/pufferfish/external/twopaco/graphdump/libgraphdump.a ../external/pufferfish/external/ntcard/libntcard.a -lgff -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex /usr/lib/x86_64-linux-gnu/libcurl.so -lz -lm /usr/lib/x86_64-linux-gnu/libstaden-read.so /usr/lib/x86_64-linux-gnu/libhtscodecs.so -llzma -lbz2 -lgomp ../external/pufferfish/src/libksw2pp.a libalevin_core.a -ltbb -ltbbmalloc -ljemalloc -lrt -ldl
make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
[100%] Built target salmon
make[3]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/CMakeFiles 0
make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
mv doc/source/license.rst doc/ # unused
PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml doc/source doc/build/html
Running Sphinx v8.1.3
loading translations [en]... done
making output directory... done
WARNING: html_static_path entry '_static' does not exist
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
building [mo]: targets for 0 po files that are out of date
writing output...
building [html]: targets for 6 source files that are out of date
updating environment: [new config] 6 added, 0 changed, 0 removed
reading sources... [ 17%] alevin
reading sources... [ 33%] building
reading sources... [ 50%] file_formats
reading sources... [ 67%] index
reading sources... [ 83%] library_type
reading sources... [100%] salmon
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:36: WARNING: Title underline too short.
Providing multiple read files to Alevin
------------ [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:36: WARNING: Title underline too short.
Providing multiple read files to Alevin
------------ [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:56: WARNING: Explicit markup ends without a blank line; unexpected unindent. [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:79: WARNING: Block quote ends without a blank line; unexpected unindent. [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:83: WARNING: Title overline too short.
""""""""""""
``--whitelist``
"""""""""""" [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:83: WARNING: Title overline too short.
""""""""""""
``--whitelist``
"""""""""""" [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:93: WARNING: Title overline too short.
""""""""""""
``--noQuant``
"""""""""""" [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:93: WARNING: Title overline too short.
""""""""""""
``--noQuant``
"""""""""""" [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:99: WARNING: Title overline too short.
""""""""""""
``--noDedup``
"""""""""""" [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:99: WARNING: Title overline too short.
""""""""""""
``--noDedup``
"""""""""""" [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:127: WARNING: Title overline too short.
""""""""""""
``--dumpBfh``
"""""""""""" [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:127: WARNING: Title overline too short.
""""""""""""
``--dumpBfh``
"""""""""""" [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:133: WARNING: Title overline too short.
""""""""""""
``--dumpFeatures``
"""""""""""" [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:133: WARNING: Title overline too short.
""""""""""""
``--dumpFeatures``
"""""""""""" [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:139: WARNING: Title overline too short.
""""""""""""
``--dumpMtx``
"""""""""""" [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:139: WARNING: Title overline too short.
""""""""""""
``--dumpMtx``
"""""""""""" [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:155: WARNING: Title overline too short.
""""""""""""""""""""""
``--numCellBootstraps``
"""""""""""""""""""""" [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:155: WARNING: Title overline too short.
""""""""""""""""""""""
``--numCellBootstraps``
"""""""""""""""""""""" [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:214: WARNING: Title underline too short.
Output Quality Check
------------- [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:214: WARNING: Title underline too short.
Output Quality Check
------------- [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:263: WARNING: Title underline too short.
BibTex
---- [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:263: WARNING: Title underline too short.
BibTex
---- [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:297: WARNING: Duplicate explicit target name: "swish". [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:299: WARNING: Footnote [#] is not referenced. [ref.footnote]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:301: WARNING: Footnote [#] is not referenced. [ref.footnote]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:303: WARNING: Footnote [#] is not referenced. [ref.footnote]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:305: WARNING: Footnote [#] is not referenced. [ref.footnote]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:307: WARNING: Footnote [#] is not referenced. [ref.footnote]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:309: WARNING: Footnote [#] is not referenced. [ref.footnote]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/alevin.rst:311: WARNING: Footnote [#] is not referenced. [ref.footnote]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/salmon.rst:2: WARNING: Duplicate explicit target name: "here". [docutils]
/build/reproducible-path/salmon-1.10.2+ds1/doc/source/salmon.rst:2: WARNING: Duplicate explicit target name: "here". [docutils]
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets...
copying static files...
Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/language_data.js
Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/basic.css
Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/documentation_options.js
Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/sidebar.js
Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/classic.css
Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/sidebar.js
copying static files: done
copying extra files...
copying extra files: done
copying assets: done
writing output... [ 17%] alevin
writing output... [ 33%] building
writing output... [ 50%] file_formats
writing output... [ 67%] index
writing output... [ 83%] library_type
writing output... [100%] salmon
generating indices... genindex done
writing additional pages... search done
copying images... [100%] ReadLibraryIllustration.png
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 33 warnings.
The HTML pages are in doc/build/html.
mv doc/license.rst doc/source/
cd obj*/src && \
help2man --no-discard-stderr --no-info --name="highly-accurate, transcript-level quantification estimates from RNA-seq data"\
./salmon > ../../debian/salmon.1 && \
for option in index quant swim; do help2man --no-discard-stderr \
--version-string="1.10.2+ds1" --no-info "./salmon --no-version-check ${option}" \
--include=../../debian/salmon-${option}-man-include \
> ../../debian/salmon-${option}.1; done
make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1'
dh_auto_test --no-parallel
cd obj-x86_64-linux-gnu && make -j1 test ARGS\+=--verbose ARGS\+=-j1
make[2]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
Running tests...
/usr/bin/ctest --force-new-ctest-process --verbose -j1
UpdateCTestConfiguration from :/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/DartConfiguration.tcl
UpdateCTestConfiguration from :/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/DartConfiguration.tcl
Test project /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: unit_tests
1: Test command: /usr/bin/cmake "-DTOPLEVEL_DIR=/build/reproducible-path/salmon-1.10.2+ds1" "-P" "/build/reproducible-path/salmon-1.10.2+ds1/cmake/UnitTests.cmake"
1: Working Directory: /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src
1: Test timeout computed to be: 10000000
1: -- For unit tests, will set working directory to /build/reproducible-path/salmon-1.10.2+ds1/tests
1: ===============================================================================
1: All tests passed (1996327 assertions in 4 test cases)
1:
1/2 Test #1: unit_tests ....................... Passed 1.06 sec
test 2
Start 2: salmon_read_test_quasi
2: Test command: /usr/bin/cmake "-DTOPLEVEL_DIR=/build/reproducible-path/salmon-1.10.2+ds1" "-P" "/build/reproducible-path/salmon-1.10.2+ds1/cmake/TestSalmonQuasi.cmake"
2: Working Directory: /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src
2: Test timeout computed to be: 10000000
2: sample_data/
2: sample_data/reads_2.fastq
2: sample_data/sample_alignments.bam
2: sample_data/transcripts.fasta
2: sample_data/reads_1.fastq
2: index ["sample_salmon_quasi_index"] did not previously exist . . . creating it
2: [2025-03-14 09:17:43.678] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.
2: [2025-03-14 09:17:43.678] [jLog] [info] building index
2: out : sample_salmon_quasi_index
2: [2025-03-14 09:17:43.678] [puff::index::jointLog] [info] Running fixFasta
2:
2: [Step 1 of 4] : counting k-mers
2:
2: [2025-03-14 09:17:43.701] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
2: [2025-03-14 09:17:43.701] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts
2: wrote 15 cleaned references
2: [2025-03-14 09:17:43.702] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
2: [2025-03-14 09:17:43.703] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20
2: Threads = 2
2: Vertex length = 31
2: Hash functions = 5
2: Filter size = 1048576
2: Capacity = 2
2: Files:
2: sample_salmon_quasi_index/ref_k31_fixed.fa
2: --------------------------------------------------------------------------------
2: Round 0, 0:1048576
2: Pass Filling Filtering
2: 1 0 0
2: 2 0 0
2: True junctions count = 14
2: False junctions count = 18
2: Hash table size = 32
2: Candidate marks count = 57
2: --------------------------------------------------------------------------------
2: Reallocating bifurcations time: 0
2: True marks count: 51
2: Edges construction time: 0
2: --------------------------------------------------------------------------------
2: Distinct junctions = 14
2:
2: TwoPaCo::buildGraphMain:: allocated with scalable_malloc; freeing.
2: TwoPaCo::buildGraphMain:: Calling scalable_allocation_command(TBBMALLOC_CLEAN_ALL_BUFFERS, 0);
2: allowedIn: 12
2: Max Junction ID: 70
2: seen.size():569 kmerInfo.size():71
2: approximateContigTotalLength: 17465
2: counters for complex kmers:
2: (prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0
2: contig count: 24 element count: 19592 complex nodes: 0
2: # of ones in rank vector: 23
2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory sample_salmon_quasi_index
2: size = 19592
2: -----------------------------------------
2: | Loading contigs | Time = 100.87 us
2: -----------------------------------------
2: size = 19592
2: -----------------------------------------
2: | Loading contig boundaries | Time = 57.921 us
2: -----------------------------------------
2: Number of ones: 23
2: Number of ones per inventory item: 512
2: Inventory entries filled: 1
2: 23
2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] contig count for validation: 23
2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Total # of Contigs : 23
2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Total # of numerical Contigs : 23
2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Total # of contig vec entries: 36
2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] bits per offset entry 6
2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Done constructing the contig vector. 24
2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] # segments = 23
2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] total length = 19,592
2: [2025-03-14 09:17:43.837] [puff::index::jointLog] [info] Reading the reference files ...
2: [2025-03-14 09:17:43.860] [puff::index::jointLog] [info] positional integer width = 15
2: [2025-03-14 09:17:43.860] [puff::index::jointLog] [info] seqSize = 19,592
2: [2025-03-14 09:17:43.860] [puff::index::jointLog] [info] rankSize = 19,592
2: [2025-03-14 09:17:43.860] [puff::index::jointLog] [info] edgeVecSize = 0
2: [2025-03-14 09:17:43.860] [puff::index::jointLog] [info] num keys = 18,902
2:
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2: [2025-03-14 09:17:44.192] [puff::index::jointLog] [info] mphf size = 0.0125198 MB
2: [2025-03-14 09:17:44.192] [puff::index::jointLog] [info] chunk size = 9,796
2: [2025-03-14 09:17:44.192] [puff::index::jointLog] [info] chunk 0 = [0, 9,796)
2: [2025-03-14 09:17:44.192] [puff::index::jointLog] [info] chunk 1 = [9,796, 19,562)
2: [2025-03-14 09:17:44.203] [puff::index::jointLog] [info] finished populating pos vector
2: [2025-03-14 09:17:44.203] [puff::index::jointLog] [info] writing index components
2: [2025-03-14 09:17:44.204] [puff::index::jointLog] [info] finished writing dense pufferfish index
2: [2025-03-14 09:17:44.205] [jLog] [info] done building index
2: for info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000
2: Bitarray 105024 bits (100.00 %) (array + ranks )
2: final hash 0 bits (0.00 %) (nb in final hash 0)
2: ### salmon (selective-alignment-based) v1.10.2
2: ### [ program ] => salmon
2: ### [ command ] => quant
2: ### [ index ] => { sample_salmon_quasi_index }
2: ### [ libType ] => { IU }
2: ### [ mates1 ] => { reads_1.fastq }
2: ### [ mates2 ] => { reads_2.fastq }
2: ### [ output ] => { sample_salmon_quasi_quant }
2: Logs will be written to sample_salmon_quasi_quant/logs
2: -----------------------------------------
2: | Loading contig table | Time = 61.742 us
2: -----------------------------------------
2: size = 24
2: -----------------------------------------
2: | Loading contig offsets | Time = 95.196 us
2: -----------------------------------------
2: -----------------------------------------
2: | Loading reference lengths | Time = 8.882 us
2: -----------------------------------------
2: -----------------------------------------
2: | Loading mphf table | Time = 90.956 us
2: -----------------------------------------
2: size = 19592
2: Number of ones: 23
2: Number of ones per inventory item: 512
2: Inventory entries filled: 1
2: -----------------------------------------
2: | Loading contig boundaries | Time = 122.24 us
2: -----------------------------------------
2: size = 19592
2: -----------------------------------------
2: | Loading sequence | Time = 68.701 us
2: -----------------------------------------
2: size = 18902
2: -----------------------------------------
2: | Loading positions | Time = 134.73 us
2: -----------------------------------------
2: size = 28562
2: -----------------------------------------
2: | Loading reference sequence | Time = 64.912 us
2: -----------------------------------------
2: -----------------------------------------
2: | Loading reference accumulative lengths | Time = 8.9 us
2: -----------------------------------------
2: [2025-03-14 09:17:44.359] [jointLog] [info] setting maxHashResizeThreads to 20
2: [2025-03-14 09:17:44.359] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.
2: [2025-03-14 09:17:44.359] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
2: [2025-03-14 09:17:44.359] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
2: [2025-03-14 09:17:44.359] [jointLog] [info] parsing read library format
2: [2025-03-14 09:17:44.359] [jointLog] [info] There is 1 library.
2: [2025-03-14 09:17:44.359] [jointLog] [info] Loading pufferfish index
2: [2025-03-14 09:17:44.359] [jointLog] [info] Loading dense pufferfish index.
2: [2025-03-14 09:17:44.360] [jointLog] [info] done
2:
2:
2:
2:
2: [2025-03-14 09:17:44.612] [jointLog] [info] Index contained 15 targets
2: [2025-03-14 09:17:44.612] [jointLog] [info] Number of decoys : 0
2: [2025-03-14 09:17:45.174] [jointLog] [info] Computed 28 rich equivalence classes for further processing
2: [2025-03-14 09:17:45.175] [jointLog] [info] Counted 10,000 total reads in the equivalence classes
2:
2:
2:
2:
2:
2:
2:
2:
2: [2025-03-14 09:17:45.203] [jointLog] [info] Number of mappings discarded because of alignment score : 67
2: [2025-03-14 09:17:45.203] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0
2: [2025-03-14 09:17:45.203] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
2: [2025-03-14 09:17:45.203] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
2: [2025-03-14 09:17:45.208] [jointLog] [warning] Only 10000 fragments were mapped, but the number of burn-in fragments was set to 5000000.
2: The effective lengths have been computed using the observed mappings.
2:
2: [2025-03-14 09:17:45.208] [jointLog] [info] Mapping rate = 100%
2:
2: [2025-03-14 09:17:45.208] [jointLog] [info] finished quantifyLibrary()
2: [2025-03-14 09:17:45.208] [jointLog] [info] Starting optimizer
2: [2025-03-14 09:17:45.209] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
2: [2025-03-14 09:17:45.209] [jointLog] [info] iteration = 0 | max rel diff. = 14.87
2: [2025-03-14 09:17:45.211] [jointLog] [info] iteration = 100 | max rel diff. = 3.31285e-05
2: [2025-03-14 09:17:45.211] [jointLog] [info] Finished optimizer
2: [2025-03-14 09:17:45.211] [jointLog] [info] writing output
2:
2: Salmon (read) ran successfully
2/2 Test #2: salmon_read_test_quasi ........... Passed 2.55 sec
100% tests passed, 0 tests failed out of 2
Total Test time (real) = 3.61 sec
make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1'
dh_auto_install
cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/salmon-1.10.2\+ds1/debian/salmon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/salmon-1.10.2+ds1 -B/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[3]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
make[3]: Nothing to be done for 'preinstall'.
make[3]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libntcard.a
-- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets.cmake
-- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets-release.cmake
-- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libgraphdump.a
-- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets.cmake
-- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets-release.cmake
-- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libtwopaco.a
-- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake
-- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake
-- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/bin/salmon
-- Installing: /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libsalmon_core.a
Installation complete. Please ensure the following paths are set properly.
==========================================================================
Please add /usr/bin to your PATH
Please add /usr/lib to your LD_LIBRARY_PATH
==========================================================================
make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu'
rm -Rvf /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib
removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libsalmon_core.a'
removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libgraphdump.a'
removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets.cmake'
removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets-release.cmake'
removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard'
removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libtwopaco.a'
removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets.cmake'
removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets-release.cmake'
removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump'
removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libntcard.a'
removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake'
removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake'
removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco'
removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib'
make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1'
dh_install
dh_installdocs
dh_sphinxdoc
dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/copybutton.js
dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/menu.js
dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/themetoggle.js
dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/search-focus.js
dh_installchangelogs
dh_installexamples
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib64/ld-linux-x86-64.so.2
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'salmon' in '../salmon_1.10.2+ds1-1_amd64.deb'.
dpkg-deb: building package 'salmon-dbgsym' in '../salmon-dbgsym_1.10.2+ds1-1_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../salmon_1.10.2+ds1-1_amd64.buildinfo
dpkg-genchanges --build=binary -O../salmon_1.10.2+ds1-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/1830931 and its subdirectories
I: Current time: Fri Mar 14 09:19:15 -12 2025
I: pbuilder-time-stamp: 1741987155
Fri Mar 14 21:19:17 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net.
Fri Mar 14 21:19:17 UTC 2025 I: Preparing to do remote build '2' on ionos5-amd64.debian.net.
Fri Mar 14 21:23:37 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net.
Fri Mar 14 21:23:37 UTC 2025 I: salmon_1.10.2+ds1-1_amd64.changes:
Format: 1.8
Date: Wed, 16 Aug 2023 13:09:23 +0200
Source: salmon
Binary: salmon salmon-dbgsym
Architecture: amd64
Version: 1.10.2+ds1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <crusoe@debian.org>
Description:
salmon - wicked-fast transcript quantification from RNA-seq data
Closes: 1043107
Changes:
salmon (1.10.2+ds1-1) unstable; urgency=medium
.
* New upstream version
Closes: #1043107
* Standards-Version: 4.6.2 (routine-update)
Checksums-Sha1:
457a373922a4992bdedb66c28ca1e6eb654a8dd9 43075684 salmon-dbgsym_1.10.2+ds1-1_amd64.deb
2713ff7eb8dd565d4ea0048add8720020a812d58 11655 salmon_1.10.2+ds1-1_amd64.buildinfo
1c40ab1df140890fb94b7678c074ed6550052226 3419988 salmon_1.10.2+ds1-1_amd64.deb
Checksums-Sha256:
884a5194b2ef63a14f2322a2d1b49ccce4b74c271caf7ce3944a686c79a0d6ad 43075684 salmon-dbgsym_1.10.2+ds1-1_amd64.deb
b1d1c05f70361bb4a158897baec6c9655289088ec21520e4693e051266ef094f 11655 salmon_1.10.2+ds1-1_amd64.buildinfo
b76bfe981308a4755e93a875938f1d5009393132040dbc22cb8dbf47ad655bbd 3419988 salmon_1.10.2+ds1-1_amd64.deb
Files:
314e03b3b69de6b22aa6ca69f9c8d153 43075684 debug optional salmon-dbgsym_1.10.2+ds1-1_amd64.deb
b89a53423a4f72a5cd4ece333ee4cf43 11655 science optional salmon_1.10.2+ds1-1_amd64.buildinfo
0b135e9181cf554e3d512ea87ee14e7a 3419988 science optional salmon_1.10.2+ds1-1_amd64.deb
Fri Mar 14 21:23:39 UTC 2025 I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_5-33799.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.LV3asmU0/salmon_1.10.2+ds1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.LV3asmU0/salmon_1.10.2+ds1-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.LV3asmU0/salmon_1.10.2+ds1-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.LV3asmU0/b1/salmon_1.10.2+ds1-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.LV3asmU0/b2/salmon_1.10.2+ds1-1_amd64.changes
## close_archive (total time: 0.000s)
0.000s 6 calls diffoscope.comparators.xz.XzContainer
0.000s 2 calls diffoscope.comparators.deb.DebContainer
0.000s 4 calls diffoscope.comparators.tar.TarContainer
0.000s 2 calls diffoscope.comparators.deb.DebTarContainer
## command (total time: 0.695s)
0.456s 6 calls xz
0.092s 6 calls diff
0.073s 2 calls cmp
0.073s 2 calls cmp (external)
0.001s 14 calls cmp (internal)
## compare_files (cumulative) (total time: 3.202s)
1.009s 1 call abc.DotChangesFile
0.904s 1 call abc.DebFile
0.848s 2 calls abc.XzFile
0.332s 1 call abc.DebDataTarFile
0.074s 1 call abc.TextFile
0.029s 1 call abc.TarFile
0.006s 1 call abc.Md5sumsFile
## container_extract (total time: 0.550s)
0.456s 6 calls diffoscope.comparators.xz.XzContainer
0.062s 98 calls diffoscope.comparators.deb.DebTarContainer
0.029s 8 calls diffoscope.comparators.deb.DebContainer
0.003s 6 calls diffoscope.comparators.tar.TarContainer
## diff (total time: 0.275s)
0.275s 46 calls linediff
## has_same_content_as (total time: 0.075s)
0.056s 2 calls abc.DebFile
0.018s 1 call abc.DebDataTarFile
0.000s 4 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink
0.000s 3 calls abc.TextFile
0.000s 2 calls abc.Md5sumsFile
0.000s 1 call diffoscope.comparators.binary.FilesystemFile
0.000s 2 calls abc.XzFile
0.000s 1 call abc.DotChangesFile
0.000s 1 call abc.TarFile
## main (total time: 95.782s)
95.782s 2 calls outputs
0.000s 1 call cleanup
## open_archive (total time: 0.000s)
0.000s 6 calls diffoscope.comparators.xz.XzContainer
0.000s 4 calls diffoscope.comparators.tar.TarContainer
0.000s 2 calls diffoscope.comparators.deb.DebContainer
0.000s 2 calls diffoscope.comparators.deb.DebTarContainer
## output (total time: 94.084s)
94.081s 1 call html
0.002s 1 call text
0.001s 1 call json
## recognizes (total time: 0.513s)
0.399s 12 calls diffoscope.comparators.binary.FilesystemFile
0.052s 546 calls diffoscope.comparators.utils.libarchive.LibarchiveMember
0.039s 108 calls diffoscope.comparators.debian.DebControlMember
0.022s 260 calls diffoscope.comparators.utils.archive.ArchiveMember
## specialize (total time: 0.789s)
0.789s 16 calls specialize
Finished with result: success
Main processes terminated with: code=exited/status=1
Service runtime: 1min 36.079s
CPU time consumed: 1min 35.945s
Fri Mar 14 21:42:42 UTC 2025 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate.
Fri Mar 14 21:42:42 UTC 2025 E: salmon failed to build reproducibly in unstable on amd64.
Fri Mar 14 21:42:46 UTC 2025 I: Submitting .buildinfo files to external archives:
Fri Mar 14 21:42:46 UTC 2025 I: Submitting 16K b1/salmon_1.10.2+ds1-1_amd64.buildinfo.asc
Fri Mar 14 21:42:53 UTC 2025 I: Submitting 16K b2/salmon_1.10.2+ds1-1_amd64.buildinfo.asc
Fri Mar 14 21:43:00 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Fri Mar 14 21:43:00 UTC 2025 I: Done submitting .buildinfo files.
Fri Mar 14 21:43:00 UTC 2025 I: Removing signed salmon_1.10.2+ds1-1_amd64.buildinfo.asc files:
removed './b1/salmon_1.10.2+ds1-1_amd64.buildinfo.asc'
removed './b2/salmon_1.10.2+ds1-1_amd64.buildinfo.asc'