Fri Mar 14 06:52:41 UTC 2025 I: starting to build salmon/trixie/amd64 on jenkins on '2025-03-14 06:52' Fri Mar 14 06:52:41 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_6/35333/console.log Fri Mar 14 06:52:41 UTC 2025 I: Downloading source for trixie/salmon=1.10.2+ds1-1 --2025-03-14 06:52:41-- 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% 400M=0s 2025-03-14 06:52:41 (400 MB/s) - ‘salmon_1.10.2+ds1-1.dsc’ saved [2558/2558] Fri Mar 14 06:52:41 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 Uploaders: Michael R. Crusoe , Kevin Murray 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: 8cb3bf45b7d8ffe9e3c8a72576541df2c0c547f2 5718424 salmon_1.10.2+ds1.orig.tar.xz 30674e13817eeb27ade3c0ee5073540e9cbda647 1893940 salmon_1.10.2+ds1-1.debian.tar.xz Checksums-Sha256: 895840bed22f93cb8c02ff00b9007473e291ef06b753a950ec2b75373d78219c 5718424 salmon_1.10.2+ds1.orig.tar.xz 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 -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmTcroMACgkQPCZ2P2xn 5uIu5w/+JPSxmuJiLVVlIZ7SjpjJMMgEiYMmna5OIZS+0BRh3/Y5fdXty8GHJ1ry bDntR1ondwWXHZoglZCykAtP6jWbx67/WfmnnmYqrKPP977KpbjyAJ9Grrt9nK9u VlENkkFxv0b1vLdlwuuX8dEZWz282kvJyquthYWB1oIXUIRYhBlaiuuEBQy95SS7 eEOrs6K6wxFfwFHZ4wEx8uAit/7EuFyH9uw0+WKtlfbUAEyowIAL8MwD/osP+0jd iaQo+0KOE+297HMV2gJTeAvP8kTvCBwb6NFPtUWS2zjGmipkU7lurV+gpMC0HNFw Fk/63W9Je9d6RJlpXa3grfCrwmfV2MvVjjTOBo4U/W4QvDfrqqQRQHQBxQCj9Joi O0CHb8KrH0flPsex71TREbYqZj35l9llT1AyMqJ0Q3eR2gBRgIW7nrnR/0/kTMLR oyn+ooaXEMhSLYIHmV1auVOQ4yAff/s8RiejlWCBTDuHHB1T/e4H70ZSyrCMqNyg 1l/MabEpZO6gEatn8VsehdqKDimyrunkou+VvDsvYigbIIGrgzYZNFvudXfEKRSo SDxiRAdvasN0neNqy01gepn7iSZSqKTVaTkuBKSwBpmiLEkSj/1rIYL5tGcSHBxR 7av8D94MGO6MQN5JvtR+exUKdseIMAq90NWqC9sq++WDRmeTGkM= =HBVp -----END PGP SIGNATURE----- Fri Mar 14 06:52:41 UTC 2025 I: Checking whether the package is not for us Fri Mar 14 06:52:41 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net. Fri Mar 14 06:52:41 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Fri Mar 14 06:56:58 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Apr 16 01:15:41 -12 2026 I: pbuilder-time-stamp: 1776345341 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/642106/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=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='77b4c6fbd19847a7874f412134be3c22' 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='642106' 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.wHaKwDZB/pbuilderrc_zc4f --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wHaKwDZB/b1 --logfile b1/build.log salmon_1.10.2+ds1-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/642106/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 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 ... 19802 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} libicu72{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 153 MB of archives. After unpacking 814 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 media-types all 13.0.0 [29.3 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025a-2 [259 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.2-1 [745 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.2-2 [28.1 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.4.1-1 [1427 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20241223 [164 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-7 [294 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.31.6-1 [2268 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 46 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-1 [109 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.8.0-1 [67.7 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.12.1-3 [369 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.50.0-2 [154 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.31.6-1 [12.0 MB] Get: 66 http://deb.debian.org/debian trixie/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-4 [539 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 73 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 docutils-doc all 0.21.2+dfsg-2 [1122 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 icu-devtools amd64 72.1-6 [210 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-4.1+b1 [10.6 MB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libboost-atomic1.83.0 amd64 1.83.0-4.1+b1 [234 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libboost-atomic1.83-dev amd64 1.83.0-4.1+b1 [236 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-4.1+b1 [240 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libboost-chrono1.83-dev amd64 1.83.0-4.1+b1 [246 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libboost-date-time1.83.0 amd64 1.83.0-4.1+b1 [230 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libboost-serialization1.83.0 amd64 1.83.0-4.1+b1 [334 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libboost-serialization1.83-dev amd64 1.83.0-4.1+b1 [373 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libboost-date-time1.83-dev amd64 1.83.0-4.1+b1 [240 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-4.1+b1 [282 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libboost-system1.83.0 amd64 1.83.0-4.1+b1 [231 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libboost-system1.83-dev amd64 1.83.0-4.1+b1 [232 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-4.1+b1 [298 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get: 104 http://deb.debian.org/debian trixie/main amd64 libboost-regex1.83.0 amd64 1.83.0-4.1+b1 [330 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libicu-dev amd64 72.1-6 [10.4 MB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libboost-regex1.83-dev amd64 1.83.0-4.1+b1 [347 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libboost-iostreams1.83-dev amd64 1.83.0-4.1+b1 [261 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libboost-iostreams-dev amd64 1.83.0.2+b2 [3580 B] Get: 109 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.1+b1 [347 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83-dev amd64 1.83.0-4.1+b1 [376 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 112 http://deb.debian.org/debian trixie/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B] Get: 113 http://deb.debian.org/debian trixie/main amd64 libboost-thread1.83.0 amd64 1.83.0-4.1+b1 [270 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libboost-thread1.83-dev amd64 1.83.0-4.1+b1 [277 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Get: 116 http://deb.debian.org/debian trixie/main amd64 libboost-timer1.83.0 amd64 1.83.0-4.1+b1 [235 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libboost-timer1.83-dev amd64 1.83.0-4.1+b1 [237 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libboost-timer-dev amd64 1.83.0.2+b2 [3716 B] Get: 119 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libbwa-dev amd64 0.7.18-1 [156 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libcares2 amd64 1.34.4-2.1 [97.9 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libcereal-dev amd64 1.3.2+dfsg-5 [221 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.11.0-1 [131 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.11.0-1 [29.3 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libidn2-dev amd64 2.3.8-1 [102 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libnghttp3-dev amd64 1.8.0-1 [91.3 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.11.0-1 [34.0 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libngtcp2-dev amd64 1.11.0-1 [179 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.12.1-3 [480 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libdivsufsort3 amd64 2.0.1-6+b1 [45.9 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libdivsufsort-dev amd64 2.0.1-6+b1 [19.1 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libfmt-dev amd64 10.1.1+ds1-4 [177 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libgff-dev amd64 2.0.0-3 [154 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libhtscodecs-dev amd64 1.6.1-2 [3000 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.12.0-1 [164 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libjellyfish-2.0-2 amd64 2.3.1-4+b1 [67.3 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libjellyfish-2.0-dev amd64 2.3.1-4+b1 [138 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libjemalloc2 amd64 5.3.0-3 [274 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libjemalloc-dev amd64 5.3.0-3 [490 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.4-1 [323 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 node-xtend all 4.0.2-3 [3932 B] Get: 175 http://deb.debian.org/debian trixie/main amd64 node-corepack all 0.24.0-4 [704 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 nodejs amd64 20.18.3+dfsg-1 [349 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 node-acorn all 8.8.1+ds+~cs25.17.7-2 [128 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 node-cjs-module-lexer all 1.2.3+dfsg-1 [30.6 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 node-balanced-match all 2.0.0-1 [4872 B] Get: 180 http://deb.debian.org/debian trixie/main amd64 node-brace-expansion all 2.0.1+~1.1.0-1 [7912 B] Get: 181 http://deb.debian.org/debian trixie/main amd64 node-minimatch all 9.0.3-5 [76.7 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 node-undici all 7.3.0+dfsg1+~cs24.12.11-1 [333 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libnode115 amd64 20.18.3+dfsg-1 [12.1 MB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libpthread-stubs0-dev amd64 0.5-1 [5168 B] Get: 185 http://deb.debian.org/debian trixie/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 libspdlog1.15 amd64 1:1.15.1+ds-1 [108 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 libspdlog-dev amd64 1:1.15.1+ds-1 [90.8 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 libstaden-read14t64 amd64 1.15.0-1.1+b2 [268 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 libstaden-read-dev amd64 1.15.0-1.1+b2 [347 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 libtbbbind-2-5 amd64 2022.0.0-2 [14.6 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 libtbbmalloc2 amd64 2022.0.0-2 [49.3 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 libtbb12 amd64 2022.0.0-2 [91.0 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 libtbb-dev amd64 2022.0.0-2 [199 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 libtclap-dev amd64 1.2.5-1+b2 [3359 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 node-commander all 9.4.1-1 [65.3 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 node-mj-context-menu all 0.9.1+ds-2 [69.9 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 node-speech-rule-engine all 4.0.7+~0.1.31-2 [532 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 node-mathjax-full all 3.2.2+~cs4.2.1-4 [3660 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 python-requests-doc all 2.32.3+dfsg-4 [196 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.17.0-1 [117 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B] Get: 205 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.1-1+b1 [125 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 python3.13-doc all 3.13.2-1 [15.3 MB] Get: 209 http://deb.debian.org/debian trixie/main amd64 python3-doc all 3.13.2-2 [10.3 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 8.1.3-5 [617 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 python3-roman all 5.0-1 [10.6 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 214 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b3 [14.0 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.5-2 [107 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.10-1 [42.0 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 8.1.3-5 [468 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 python3-docs-theme all 2025.2-1 [19.4 kB] Get: 224 http://deb.debian.org/debian trixie/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-2 [1023 kB] Get: 225 http://deb.debian.org/debian trixie/main amd64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 226 http://deb.debian.org/debian trixie/main amd64 python3-sphinx-rtd-theme all 3.0.2+dfsg-2 [29.7 kB] Get: 227 http://deb.debian.org/debian trixie/main amd64 rapmap-dev all 0.15.0+dfsg-4 [193 kB] Get: 228 http://deb.debian.org/debian trixie/main amd64 sphinx-doc all 8.1.3-5 [3487 kB] Fetched 153 MB in 4s (40.7 MB/s) Preconfiguring packages ... Selecting previously unselected package fonts-lato. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19802 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.2-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.2-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.2-1_amd64.deb ... Unpacking python3.13 (3.13.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libboost-thread1.83-dev:amd64 (1.83.0-4.1+b1) ... Setting up libgnutls-openssl27t64:amd64 (3.8.9-2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up python3.13 (3.13.2-1) ... Setting up libboost-iostreams1.83-dev:amd64 (1.83.0-4.1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.2-2) ... Setting up libtbb12:amd64 (2022.0.0-2) ... Setting up libboost-iostreams-dev:amd64 (1.83.0.2+b2) ... Setting up libspdlog-dev:amd64 (1:1.15.1+ds-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (2.1.5-1+b3) ... Setting up libpsl-dev:amd64 (0.21.2-1.1+b1) ... Setting up python3-roman (5.0-1) ... Setting up python3-jinja2 (3.1.5-2) ... Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (24.2-1) ... Setting up python3-chardet (5.2.0+dfsg-2) ... Setting up libgnutls-dane0t64:amd64 (3.8.9-2) ... Setting up python3-certifi (2025.1.31+ds-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up libgssrpc4t64:amd64 (1.21.3-4) ... Setting up sphinx-common (8.1.3-5) ... Setting up python3-idna (3.10-1) ... Setting up python3-urllib3 (2.3.0-1) ... Setting up libtbb-dev:amd64 (2022.0.0-2) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.11.0-1) ... Setting up libboost-thread-dev:amd64 (1.83.0.2+b2) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-4) ... Setting up python3-imagesize (1.4.1-1) ... Setting up libgnutls28-dev:amd64 (3.8.9-2) ... Setting up libcurl4t64:amd64 (8.12.1-3) ... Setting up libkdb5-10t64:amd64 (1.21.3-4) ... Setting up python3-babel (2.17.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.1-1+b1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up libcurl3t64-gnutls:amd64 (8.12.1-3) ... Setting up debhelper (13.24.1) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.11.0-1) ... Setting up python3-requests (2.32.3+dfsg-4) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-4) ... Setting up cmake (3.31.6-1) ... Setting up krb5-multidev:amd64 (1.21.3-4) ... Setting up libstaden-read14t64:amd64 (1.15.0-1.1+b2) ... Setting up libkrb5-dev:amd64 (1.21.3-4) ... Setting up libcurl4-gnutls-dev:amd64 (8.12.1-3) ... Setting up libstaden-read-dev (1.15.0-1.1+b2) ... Setting up node-acorn (8.8.1+ds+~cs25.17.7-2) ... Setting up node-corepack (0.24.0-4) ... Setting up libnode115:amd64 (20.18.3+dfsg-1) ... Setting up nodejs (20.18.3+dfsg-1) ... update-alternatives: using /usr/bin/nodejs to provide /usr/bin/js (js) in auto mode Setting up node-speech-rule-engine (4.0.7+~0.1.31-2) ... Setting up node-mathjax-full (3.2.2+~cs4.2.1-4) ... Setting up sphinx-doc (8.1.3-5) ... Processing triggers for libc-bin (2.41-4) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-5) ... Setting up python3-docs-theme (2025.2-1) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-2) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> 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 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 value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by 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 value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by 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 value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by 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 (3.2s) -- 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 -j42 "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 -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend make -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend 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/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 -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/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/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend 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/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 src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.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[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=" make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend make -f src/CMakeFiles/UnitTestsMain.dir/build.make src/CMakeFiles/UnitTestsMain.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_basic.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/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[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_core.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/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=" 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=" make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build make -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f 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'/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' make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 2%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o [ 2%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o [ 3%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o [ 4%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o [ 7%] Building CXX object src/CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o [ 7%] 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/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_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/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 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 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/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c [ 7%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o [ 8%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o [ 8%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o [ 9%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o [ 11%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o [ 12%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o [ 12%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.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_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/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 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/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 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 [ 18%] 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/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 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 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 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 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 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/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 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 [ 20%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o [ 21%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.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/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 [ 22%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o [ 23%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o [ 24%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o [ 26%] Building CXX object src/CMakeFiles/salmon_core.dir/backtrace.cc.o [ 26%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o [ 25%] 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/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 [ 26%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o [ 26%] 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/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 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 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 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-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/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 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 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 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 [ 26%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.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 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 [ 26%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C cc1: warning: command-line option '-Wno-deprecated-copy' is valid for C++/ObjC++ but not for C [ 26%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o [ 30%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o [ 31%] 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/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 [ 32%] 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 -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 cd 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CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndex.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 -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 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 [ 28%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o [ 28%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o [ 33%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.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 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 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 [ 34%] 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 [ 35%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o [ 33%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.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 [ 35%] 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 [ 33%] 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 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-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 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 [ 36%] 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 [ 37%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.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 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/build/reproducible-path/salmon-1.10.2+ds1/src/LibraryFormat.cpp [ 39%] 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 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-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 [ 41%] 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 [ 42%] 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 [ 42%] 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 [ 43%] 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 [ 44%] 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 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-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 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-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 [ 52%] 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 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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 [ 54%] 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 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-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 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-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 [ 59%] 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 [ 59%] Built target ksw2pp_sse4 [ 59%] Built target ksw2pp_sse2 [ 60%] 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 [ 60%] 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 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 [ 61%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.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/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 [ 62%] 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 [ 63%] 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 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 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() {} | ^ /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(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' "/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' [ 64%] 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 [ 65%] 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 [ 65%] Built target ksw2pp [ 66%] 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 [ 67%] Linking CXX static library libntcard.a 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() {} | ^ /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(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' 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 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() {} | ^ /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(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' 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 /usr/bin/ranlib libntcard.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 67%] Built target ntcard 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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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/external/pufferfish/src/PufferfishTestLookup.cpp: In function 'std::vector 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 get_kmers(const std::string& fasta_file, uint32_t k) { | ~~~~~~~~~^ 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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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/PufferfishBinaryGFAReader.hpp:9: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]' 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::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; 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::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; 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::_resize_delta(size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' 3813 | return rep.template find_or_insert(std::forward(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 > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >&)' 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 > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair > >; row_it = spp::sparsegroup > >, spp::libc_allocator > > > >*; col_it = std::pair > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator > > >]' 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::_set_val(value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; value_type = std::pair > >; reference = std::pair > >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' 3813 | return rep.template find_or_insert(std::forward(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 > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; 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 = true; _T1 = long unsigned int; _T2 = std::vector >]' [-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::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >; dest_it = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, 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::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::_resize_delta(size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, 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, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair, unsigned int>; row_it = spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*; col_it = std::pair, unsigned int>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator, 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::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _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 = true; _T1 = std::vector; _T2 = unsigned int]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; mutable_value_type = std::pair > >; reference = std::pair > >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' 3813 | return rep.template find_or_insert(std::forward(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 > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; 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 = true; _T1 = long unsigned int; _T2 = std::vector >]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _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 = true; _T1 = std::vector; _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/PufferfishBinaryGFAReader.hpp:9: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]' 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::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; 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::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; 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::_resize_delta(size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' 3813 | return rep.template find_or_insert(std::forward(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 > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >&)' 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 > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair > >; row_it = spp::sparsegroup > >, spp::libc_allocator > > > >*; col_it = std::pair > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator > > >]' 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::_set_val(value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; value_type = std::pair > >; reference = std::pair > >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' 3813 | return rep.template find_or_insert(std::forward(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 > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; 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 = true; _T1 = long unsigned int; _T2 = std::vector >]' [-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::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >; dest_it = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; destructive_iterator = spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, 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::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::_resize_delta(size_type) [with Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, 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, unsigned int>, spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*, std::pair, unsigned int>*, std::input_iterator_tag, spp::libc_allocator, unsigned int> > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair, unsigned int>; row_it = spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >*; col_it = std::pair, unsigned int>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator, 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::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _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 = true; _T1 = std::vector; _T2 = 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/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::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >; dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]' 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::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; 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::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; 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::_resize_delta(size_type) [with Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::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]' 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; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /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, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >&)' 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, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::pair*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]' 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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::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]' 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; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = pufferfish::util::ContigBlock; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = pufferfish::util::ContigBlock]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:143:65: required from 'Task RefSeqConstructor::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]' 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; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = true; _T1 = unsigned int; _T2 = pufferfish::util::ContigBlock]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; mutable_value_type = std::pair > >; reference = std::pair > >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' 3813 | return rep.template find_or_insert(std::forward(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 > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; 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 = true; _T1 = long unsigned int; _T2 = std::vector >]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; ExtractKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = pufferfish::BinaryGFAReader::serializeContigTable(const std::string&, const std::vector, short unsigned int> >&, const std::vector&)::VecHasher; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _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 = true; _T1 = std::vector; _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/src/FixFasta.cpp:4: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]' 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::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; 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::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; 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::_resize_delta(size_type) [with Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' 3813 | return rep.template find_or_insert(std::forward(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 > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >&)' 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 > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::pair > >; row_it = spp::sparsegroup > >, spp::libc_allocator > > > >*; col_it = std::pair > >*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator > > >]' 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::_set_val(value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; value_type = std::pair > >; reference = std::pair > >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' 3813 | return rep.template find_or_insert(std::forward(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 > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; 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 = true; _T1 = long unsigned int; _T2 = std::vector >]' [-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::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(dest_it) const [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >; dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61: required from 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::destructive_begin() [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >]' 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::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; 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::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; 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::_resize_delta(size_type) [with Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; 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::ne_iterator, bool> spp::sparse_hashtable::insert(P&&) [with P = std::__cxx11::basic_string&; Value = std::__cxx11::basic_string; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_set >::Identity; SetKey = spp::sparse_hash_set >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; typename spp::sparsetable::ne_iterator = spp::Two_d_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, 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::Identity, spp::sparse_hash_set::SetKey, EqualKey, Alloc>::const_iterator, bool> spp::sparse_hash_set::insert(P&&) [with P = std::__cxx11::basic_string&; Value = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator >; typename spp::sparse_hashtable::const_iterator = spp::Two_d_iterator, const spp::sparsegroup, spp::libc_allocator > >*, const std::__cxx11::basic_string*, std::bidirectional_iterator_tag>]' 4225 | std::pair insert(P&& obj) { return rep.insert(std::forward

(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, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >::Two_d_destructive_iterator(const spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >&)' 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, spp::sparsegroup, spp::libc_allocator > >*, std::__cxx11::basic_string*, std::input_iterator_tag, spp::libc_allocator > >' has user-provided 'spp::Two_d_destructive_iterator& spp::Two_d_destructive_iterator::operator=(const spp::Two_d_destructive_iterator&) [with T = std::__cxx11::basic_string; row_it = spp::sparsegroup, spp::libc_allocator > >*; col_it = std::__cxx11::basic_string*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator >]' 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::_init_val(mutable_value_type*, reference) [with T = std::pair > >; Alloc = spp::libc_allocator > > >; mutable_value_type = std::pair > >; reference = std::pair > >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; allocator_type = spp::libc_allocator > > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; pointer = std::pair > >*; allocator_type = spp::libc_allocator > > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair > >; T = std::pair > >; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair > >; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; reference = std::pair > >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map > >::DefaultValue; KT = long unsigned int&; Value = std::pair > >; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map > >::SelectKey; SetKey = spp::sparse_hash_map > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; value_type = std::pair > >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = std::vector >; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > > >; mapped_type = std::vector >]' 3813 | return rep.template find_or_insert(std::forward(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 > >, spp::libc_allocator > > > >::value_type' {aka 'std::pair > >'} to 'spp::sparsegroup > >, spp::libc_allocator > > > >::mutable_reference' {aka 'std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const long unsigned int; _U2 = std::vector >; 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 = true; _T1 = long unsigned int; _T2 = std::vector >]' [-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/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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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/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]': /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 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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::_set_val(value_type*, reference) [with T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; value_type = std::pair, std::vector >; reference = std::pair, std::vector >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; allocator_type = spp::libc_allocator, std::vector > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; pointer = std::pair, std::vector >*; allocator_type = spp::libc_allocator, std::vector > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; reference = std::pair, std::vector >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, std::vector >; Value = std::pair, std::vector >; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, std::vector >::SelectKey; SetKey = spp::sparse_hash_map, std::vector >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::vector > >; reference = std::pair, std::vector >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::vector >::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, std::vector >; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, std::vector >::SelectKey; SetKey = spp::sparse_hash_map, std::vector >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::vector > >; value_type = std::pair, std::vector >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = std::vector; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::vector > >; mapped_type = std::vector]' 3813 | return rep.template find_or_insert(std::forward(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::vector >, spp::libc_allocator, std::vector > > >::value_type' {aka 'std::pair, std::vector >'} to 'spp::sparsegroup, std::vector >, spp::libc_allocator, std::vector > > >::mutable_reference' {aka 'std::pair, std::vector >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = std::vector; 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 = true; _T1 = std::__cxx11::basic_string; _T2 = std::vector]' [-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::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _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 = true; _T1 = std::__cxx11::basic_string; _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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; mutable_value_type = std::pair, std::vector >; reference = std::pair, std::vector >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; allocator_type = spp::libc_allocator, std::vector > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; allocator_type = spp::libc_allocator, std::vector > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; pointer = std::pair, std::vector >*; allocator_type = spp::libc_allocator, std::vector > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, std::vector >; T = std::pair, std::vector >; Alloc = spp::libc_allocator, std::vector > >; reference = std::pair, std::vector >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, std::vector >; Value = std::pair, std::vector >; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, std::vector >::SelectKey; SetKey = spp::sparse_hash_map, std::vector >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::vector > >; reference = std::pair, std::vector >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::vector >::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, std::vector >; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, std::vector >::SelectKey; SetKey = spp::sparse_hash_map, std::vector >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::vector > >; value_type = std::pair, std::vector >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = std::vector; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::vector > >; mapped_type = std::vector]' 3813 | return rep.template find_or_insert(std::forward(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::vector >, spp::libc_allocator, std::vector > > >::value_type' {aka 'std::pair, std::vector >'} to 'spp::sparsegroup, std::vector >, spp::libc_allocator, std::vector > > >::mutable_reference' {aka 'std::pair, std::vector >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _U2 = std::vector; 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 = true; _T1 = std::__cxx11::basic_string; _T2 = std::vector]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _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 = true; _T1 = std::__cxx11::basic_string; _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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = true; _T1 = unsigned int; _T2 = unsigned int]' [-Wcast-user-defined] 1339 | ::new (p) value_type(std::move((mutable_reference)val)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 68%] 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' [ 68%] Built target graphdump 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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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/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::transform(const unsigned char*, size_t) [with T = long unsigned int; long unsigned int O = 0]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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::transform(const unsigned char*, size_t) [with T = unsigned int; long unsigned int O = 256]', inlined from 'digestpp::detail::sha2_provider::update(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::update(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::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& digestpp::hasher::absorb(IT, IT) [with IT = __gnu_cxx::__normal_iterator >; HashProvider = digestpp::detail::sha2_provider; 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(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++; | ^~~~ [ 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 [ 71%] Linking CXX static library libUnitTestsMain.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/UnitTestsMain.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/UnitTestsMain.dir/link.txt --verbose=1 [ 72%] 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 libUnitTestsMain.a CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o /usr/bin/ranlib libUnitTestsMain.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 72%] Built target UnitTestsMain make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.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/unitTests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 73%] Building CXX object src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o [ 74%] 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/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 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 [ 76%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o [ 76%] 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 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 /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 /usr/bin/ranlib libpuffer.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 76%] Built target puffer 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = delete; | ^ /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:198:22: note: remove the '< >' [ 77%] Linking CXX executable unitTests cd /build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitTests.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 -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 make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 77%] Built target unitTests [ 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' [ 78%] Built target twopaco 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=" make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-x86_64-linux-gnu' [ 81%] Building CXX object src/CMakeFiles/salmon.dir/DedupUMI.cpp.o [ 81%] Building CXX object src/CMakeFiles/salmon.dir/EMUtils.cpp.o [ 81%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o [ 83%] Building CXX object src/CMakeFiles/salmon.dir/WhiteList.cpp.o [ 83%] Building CXX object src/CMakeFiles/salmon.dir/Alevin.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 [ 84%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o [ 84%] 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 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-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 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-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 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-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 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-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 [ 89%] 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 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-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 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-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 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-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 [ 91%] Building CXX object src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o [ 92%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantMerge.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 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src/CMakeFiles/salmon.dir/FASTAParser.cpp.o [ 94%] 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/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 [ 95%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.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/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 [ 97%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o [ 97%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o [ 98%] 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/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 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 [ 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/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/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 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 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 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 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/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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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 >&)': /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, | ~~~~~~~~~~~~~~~~^~~~~~~ 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() {} | ^ /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(const registry_t&) = 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/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() {} | ^ /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(const registry_t&) = 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() {} | ^ /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(const registry_t&) = 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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::pair&; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::pair&; Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _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 = true; _T1 = std::pair; _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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::reallocate(pointer, size_t) [with T = std::pair, unsigned int>; pointer = std::pair, 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::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::pair&; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::pair&; Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>'; use 'new' and 'delete' instead [-Wclass-memaccess] 425 | pointer res = static_cast(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, 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::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::pair&; Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::pair&; Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _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 = true; _T1 = std::pair; _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/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/AlevinUtils.hpp:47: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = std::vector; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = std::vector]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = std::vector; 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 = true; _T1 = unsigned int; _T2 = std::vector]' [-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::_set_val(value_type*, reference) [with T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; value_type = std::pair, std::pair > >; reference = std::pair, std::pair > >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; allocator_type = spp::libc_allocator, std::pair > > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; pointer = std::pair, std::pair > >*; allocator_type = spp::libc_allocator, std::pair > > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, std::pair > >; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::pair >, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; value_type = std::pair, std::pair > >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = std::pair >; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; mapped_type = std::pair >]' 3813 | return rep.template find_or_insert(std::forward(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 > >, spp::libc_allocator, std::pair > > > >::value_type' {aka 'std::pair, std::pair > >'} to 'spp::sparsegroup, std::pair > >, spp::libc_allocator, std::pair > > > >::mutable_reference' {aka 'std::pair, std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = std::pair >; 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 = true; _T1 = std::vector; _T2 = std::pair >]' [-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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = short unsigned int&; Key = short unsigned int; T = short unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = short unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _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 = true; _T1 = std::vector; _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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = std::vector; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = std::vector]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = std::vector; 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 = true; _T1 = unsigned int; _T2 = std::vector]' [-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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; mutable_value_type = std::pair, std::pair > >; reference = std::pair, std::pair > >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; allocator_type = spp::libc_allocator, std::pair > > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; allocator_type = spp::libc_allocator, std::pair > > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; pointer = std::pair, std::pair > >*; allocator_type = spp::libc_allocator, std::pair > > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, std::pair > >; T = std::pair, std::pair > >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, std::pair > >; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; reference = std::pair, std::pair > >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, std::pair >, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, std::pair > >; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, std::pair >, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; value_type = std::pair, std::pair > >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = std::pair >; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, std::pair > > >; mapped_type = std::pair >]' 3813 | return rep.template find_or_insert(std::forward(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 > >, spp::libc_allocator, std::pair > > > >::value_type' {aka 'std::pair, std::pair > >'} to 'spp::sparsegroup, std::pair > >, spp::libc_allocator, std::pair > > > >::mutable_reference' {aka 'std::pair, std::pair > >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _U2 = std::pair >; 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 = true; _T1 = std::vector; _T2 = std::pair >]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = short unsigned int&; Key = short unsigned int; T = short unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = short unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int, boost::hash > >::DefaultValue; KT = std::vector&; Value = std::pair, unsigned int>; Key = std::vector; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::vector&; Key = std::vector; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::vector; _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 = true; _T1 = std::vector; _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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = true; _T1 = 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 >&, 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'} [-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){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::move(size_type, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int; reference = std::pair, 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::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::_maybe_shrink() [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::resize(size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::resize(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::reserve(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _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 = true; _T1 = std::pair; _T2 = 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/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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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/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::reallocate(pointer, size_t) [with T = std::pair, unsigned int>; pointer = std::pair, 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::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::move(size_type, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int; reference = std::pair, 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::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::_maybe_shrink() [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::resize(size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::resize(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::reserve(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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, unsigned int>'; use 'new' and 'delete' instead [-Wclass-memaccess] 425 | pointer res = static_cast(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, 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::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::move(size_type, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; size_type = long unsigned int; reference = std::pair, 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::_move_from(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::sparse_hashtable(MoveDontCopyT, spp::sparse_hashtable&, size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::_maybe_shrink() [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::resize(size_type) [with Value = std::pair, unsigned int>; Key = std::pair; HashFcn = boost::hash >; ExtractKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SelectKey; SetKey = spp::sparse_hash_map, unsigned int, boost::hash > >::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::resize(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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::reserve(size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, 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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::pair; _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 = true; _T1 = std::pair; _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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _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 = true; _T1 = std::__cxx11::basic_string; _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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = long unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = long unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_set_val(value_type*, reference) [with T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; value_type = std::pair, long unsigned int>; reference = std::pair, 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; pointer = std::pair, long unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, long unsigned int>; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, long unsigned int>::DefaultValue; KT = const std::__cxx11::basic_string&; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = long unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; mapped_type = long unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, long unsigned int>, spp::libc_allocator, long unsigned int> > >::value_type' {aka 'std::pair, long unsigned int>'} to 'spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::mutable_reference' {aka 'std::pair, long unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _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 = true; _T1 = std::__cxx11::basic_string; _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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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/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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _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 = true; _T1 = std::__cxx11::basic_string; _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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = unsigned int&; Value = std::pair; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = long unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = long unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; mutable_value_type = std::pair, long unsigned int>; reference = std::pair, 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::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; allocator_type = spp::libc_allocator, long unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; pointer = std::pair, long unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, long unsigned int>; T = std::pair, long unsigned int>; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, long unsigned int>; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, long unsigned int>::DefaultValue; KT = const std::__cxx11::basic_string&; Value = std::pair, long unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, long unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, long unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = long unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, long unsigned int> >; mapped_type = long unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, long unsigned int>, spp::libc_allocator, long unsigned int> > >::value_type' {aka 'std::pair, long unsigned int>'} to 'spp::sparsegroup, long unsigned int>, spp::libc_allocator, long unsigned int> > >::mutable_reference' {aka 'std::pair, long unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _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 = true; _T1 = std::__cxx11::basic_string; _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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = true; _T1 = long unsigned int; _T2 = 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/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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = true; _T1 = long unsigned int; _T2 = 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/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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = const short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const short unsigned int&; Key = short unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = const short unsigned int&; Value = std::pair; Key = short unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = const short unsigned int&; Key = short unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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&, spp::sparse_hash_map, unsigned int>&, AlevinOpts&, GZipWriter&, std::vector >&, std::vector&, CFreqMapT&, size_t) [with ProtocolT = alevin::protocols::DropSeq; EqMapT = libcuckoo::cuckoohash_map, std::allocator >, 4>; CFreqMapT = tsl::array_map; 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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _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 = true; _T1 = std::__cxx11::basic_string; _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&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::DropSeq; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; 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&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' 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' [-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&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::InDropV2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::InDropV2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; 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&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::InDropV2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' 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' [-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&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CITESeq; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CITESeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; 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&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CITESeq; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' 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' [-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&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::ChromiumV3; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::ChromiumV3; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; 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&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::ChromiumV3; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' 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' [-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&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Chromium; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Chromium; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; 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&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::Chromium; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' 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' [-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&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Gemcode; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Gemcode; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; 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&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::Gemcode; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' 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' [-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&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CELSeq; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CELSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; 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&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' 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' [-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&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CELSeq2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CELSeq2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; 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&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' 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' [-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&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SplitSeqV1; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SplitSeqV1; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; 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&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV1; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' 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' [-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&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SplitSeqV2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SplitSeqV2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; 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&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' 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' [-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&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::QuartzSeq2; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::QuartzSeq2; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; 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&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::QuartzSeq2; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' 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' [-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&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SciSeq3; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SciSeq3; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; 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&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::SciSeq3; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' 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' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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&, spp::sparse_hash_map, unsigned int>&, AlevinOpts&, GZipWriter&, std::vector >&, std::vector&, CFreqMapT&, size_t) [with ProtocolT = alevin::protocols::DropSeq; EqMapT = libcuckoo::cuckoohash_map, std::allocator >, 4>; CFreqMapT = tsl::array_map; 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, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _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 = true; _T1 = std::__cxx11::basic_string; _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/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Custom; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Custom; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; 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&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::Custom; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' 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' [-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&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CustomGeometry; CFreqMapT = tsl::array_map; TrueBcsT = std::unordered_set >; SoftMapT = std::unordered_map, std::vector, double> > >]': /build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16: required from 'void processBarcodes(std::vector >&, std::vector >&, AlevinOpts&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CustomGeometry; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; CFreqMapT = tsl::array_map; 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&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector >, std::vector >, std::unique_ptr&) [with ProtocolT = alevin::protocols::CustomGeometry; OrderedOptionsT = boost::program_options::basic_parsed_options; std::string = std::__cxx11::basic_string]' 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' [-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/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::DropSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::DropSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CITESeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CITESeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CITESeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CITESeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CITESeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::InDropV2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDropV2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDropV2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::InDropV2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::InDropV2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDropV2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::InDropV2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::InDropV2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::ChromiumV3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::ChromiumV3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::ChromiumV3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::ChromiumV3; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::ChromiumV3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Chromium; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::Chromium; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Chromium; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Chromium; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::Chromium; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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/AlignmentLibrary.hpp:19: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Gemcode; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::Gemcode; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Gemcode; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Gemcode; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::Gemcode; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CELSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CELSeq; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CELSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CELSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CELSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CELSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SplitSeqV1; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV1; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV1; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV1; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::SplitSeqV1; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV1; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV1; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV1; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SplitSeqV2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::SplitSeqV2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::SplitSeqV2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::QuartzSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::QuartzSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::QuartzSeq2; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::QuartzSeq2; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::QuartzSeq2; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SciSeq3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SciSeq3; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SciSeq3; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::SciSeq3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::SciSeq3; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SciSeq3; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SciSeq3; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::SciSeq3; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::Custom; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::Custom; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::Custom; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::Custom; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::Custom; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::CustomGeometry; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CustomGeometry; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, IndexT*, std::vector&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts&, MappingStatistics&) [with IndexT = PufferfishIndex; ProtocolT = alevin::protocols::CustomGeometry; alevin::paired_parser = fastx_parser::FastxParser; ReadExperimentT = ReadExperiment >; alevin::AlnGroupVec = std::vector, std::allocator > >; std::ofstream = std::basic_ofstream]': /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33: required from 'sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, AlevinOpts&, MappingStatistics&):: [with auto:7 = fastx_parser::FastxParser; 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&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, FragmentLengthDistribution&, SalmonOpts&, std::atomic&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector > >&, AlevinOpts&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; std::ofstream = std::basic_ofstream; 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&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::CustomGeometry; ReadExperimentT = ReadExperiment >; uint32_t = unsigned int]' 2094 | sc_align_read_library(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&, SalmonOpts&, boost::program_options::parsed_options&, std::unique_ptr&) [with ProtocolT = alevin::protocols::CustomGeometry; boost::program_options::parsed_options = boost::program_options::basic_parsed_options]' 2521 | bool mapping_ok = do_sc_align(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); | ^ /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& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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, 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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_set_val(value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_set_val(value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_map; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_map]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_map; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_map]' [-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::_init_val(mutable_value_type*, reference) [with T = std::pair; Alloc = spp::libc_allocator >; mutable_value_type = std::pair; reference = std::pair&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1390:18: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; size_type = unsigned char; realloc_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; allocator_type = spp::libc_allocator >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; pointer = std::pair*; allocator_type = spp::libc_allocator >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; reference = std::pair&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map::DefaultValue; KT = long unsigned int&; Value = std::pair; Key = long unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map::SelectKey; SetKey = spp::sparse_hash_map::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; value_type = std::pair]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = long unsigned int&; Key = long unsigned int; T = unsigned int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(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, spp::libc_allocator > >::value_type' {aka 'std::pair'} to 'spp::sparsegroup, spp::libc_allocator > >::mutable_reference' {aka 'std::pair&'} 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 = 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::_init_val(mutable_value_type*, reference) [with T = std::pair >; Alloc = spp::libc_allocator > >; mutable_value_type = std::pair >; reference = std::pair >&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; allocator_type = spp::libc_allocator > >; 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; pointer = std::pair >*; allocator_type = spp::libc_allocator > >; 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair >; T = std::pair >; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair >; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; reference = std::pair >&; 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map >::DefaultValue; KT = unsigned int&; Value = std::pair >; Key = unsigned int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map >::SelectKey; SetKey = spp::sparse_hash_map >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; value_type = std::pair >]' 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = unsigned int&; Key = unsigned int; T = spp::sparse_hash_set; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator > >; mapped_type = spp::sparse_hash_set]' 3813 | return rep.template find_or_insert(std::forward(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 >, spp::libc_allocator > > >::value_type' {aka 'std::pair >'} to 'spp::sparsegroup >, spp::libc_allocator > > >::mutable_reference' {aka 'std::pair >&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const unsigned int; _U2 = spp::sparse_hash_set; 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 = true; _T1 = unsigned int; _T2 = spp::sparse_hash_set]' [-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::_set_val(value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1440:21: required from 'void spp::sparsegroup::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2647:50: required from 'int alevinQuant(AlevinOpts&, SalmonOpts&, SoftMapT&, TrueBcsT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, boost::program_options::parsed_options&, CFreqMapT&, size_t, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; boost::program_options::parsed_options = boost::program_options::basic_parsed_options; CFreqMapT = tsl::array_map; 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); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1355:41: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _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 = true; _T1 = std::__cxx11::basic_string; _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::_init_val(mutable_value_type*, reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; mutable_value_type = std::pair, unsigned int>; reference = std::pair, unsigned int>&]': /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1407:22: required from 'void spp::sparsegroup::_set_aux(allocator_type&, size_type, Val&, realloc_not_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, unsigned int> >; size_type = unsigned char; realloc_not_ok_type = spp::integral_constant]' 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::_set(allocator_type&, size_type, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; allocator_type = spp::libc_allocator, 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::value_type* spp::sparsegroup::set(allocator_type&, size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; pointer = std::pair, unsigned int>*; allocator_type = spp::libc_allocator, 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::value_type& spp::sparsetable::set(size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::_insert_at(T&, size_type, bool) [with T = std::pair, unsigned int>; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; reference = std::pair, 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_type& spp::sparse_hashtable::find_or_insert(KT&&) [with DefaultValue = spp::sparse_hash_map, unsigned int>::DefaultValue; KT = std::__cxx11::basic_string&; Value = std::pair, unsigned int>; Key = std::__cxx11::basic_string; HashFcn = spp::spp_hash >; ExtractKey = spp::sparse_hash_map, unsigned int>::SelectKey; SetKey = spp::sparse_hash_map, unsigned int>::SetKey; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; value_type = std::pair, 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::mapped_type& spp::sparse_hash_map::operator[](KT&&) [with KT = std::__cxx11::basic_string&; Key = std::__cxx11::basic_string; T = unsigned int; HashFcn = spp::spp_hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; mapped_type = unsigned int]' 3813 | return rep.template find_or_insert(std::forward(key)).second; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:2647:50: required from 'int alevinQuant(AlevinOpts&, SalmonOpts&, SoftMapT&, TrueBcsT&, spp::sparse_hash_map&, spp::sparse_hash_map, unsigned int>&, boost::program_options::parsed_options&, CFreqMapT&, size_t, std::unique_ptr&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map, std::vector, double> > >; TrueBcsT = std::unordered_set >; boost::program_options::parsed_options = boost::program_options::basic_parsed_options; CFreqMapT = tsl::array_map; 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); | ^ /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:1339:40: warning: casting 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::value_type' {aka 'std::pair, unsigned int>'} to 'spp::sparsegroup, unsigned int>, spp::libc_allocator, unsigned int> > >::mutable_reference' {aka 'std::pair, unsigned int>&'} does not use 'constexpr std::pair<_T1, _T2>::pair(const std::pair<_U1, _U2>&) [with _U1 = const std::__cxx11::basic_string; _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 = true; _T1 = std::__cxx11::basic_string; _T2 = 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/documentation_options.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/language_data.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 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 (1983205 assertions in 4 test cases) 1: 1/2 Test #1: unit_tests ....................... Passed 0.22 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: [2026-04-16 01:19:23.148] [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: [2026-04-16 01:19:23.148] [jLog] [info] building index 2: out : sample_salmon_quasi_index 2: [2026-04-16 01:19:23.148] [puff::index::jointLog] [info] Running fixFasta 2: 2: [Step 1 of 4] : counting k-mers 2: 2: [2026-04-16 01:19:23.152] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides 2: [2026-04-16 01:19:23.152] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts 2: wrote 15 cleaned references 2: [2026-04-16 01:19:23.152] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers 2: [2026-04-16 01:19:23.153] [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 = 17 2: Hash table size = 31 2: Candidate marks count = 54 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: [2026-04-16 01:19:23.175] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file. 2: [2026-04-16 01:19:23.175] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory sample_salmon_quasi_index 2: size = 19592 2: ----------------------------------------- 2: | Loading contigs | Time = 87.524 us 2: ----------------------------------------- 2: size = 19592 2: ----------------------------------------- 2: | Loading contig boundaries | Time = 61.082 us 2: ----------------------------------------- 2: Number of ones: 23 2: Number of ones per inventory item: 512 2: Inventory entries filled: 1 2: 23 2: [2026-04-16 01:19:23.175] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure. 2: [2026-04-16 01:19:23.175] [puff::index::jointLog] [info] contig count for validation: 23 2: [2026-04-16 01:19:23.175] [puff::index::jointLog] [info] Total # of Contigs : 23 2: [2026-04-16 01:19:23.175] [puff::index::jointLog] [info] Total # of numerical Contigs : 23 2: [2026-04-16 01:19:23.175] [puff::index::jointLog] [info] Total # of contig vec entries: 36 2: [2026-04-16 01:19:23.175] [puff::index::jointLog] [info] bits per offset entry 6 2: [2026-04-16 01:19:23.175] [puff::index::jointLog] [info] Done constructing the contig vector. 24 2: [2026-04-16 01:19:23.175] [puff::index::jointLog] [info] # segments = 23 2: [2026-04-16 01:19:23.175] [puff::index::jointLog] [info] total length = 19,592 2: [2026-04-16 01:19:23.175] [puff::index::jointLog] [info] Reading the reference files ... 2: [2026-04-16 01:19:23.176] [puff::index::jointLog] [info] positional integer width = 15 2: [2026-04-16 01:19:23.176] [puff::index::jointLog] [info] seqSize = 19,592 2: [2026-04-16 01:19:23.176] [puff::index::jointLog] [info] rankSize = 19,592 2: [2026-04-16 01:19:23.176] [puff::index::jointLog] [info] edgeVecSize = 0 2: [2026-04-16 01:19:23.176] [puff::index::jointLog] [info] num keys = 18,902 2: [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building 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remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec 2: [2026-04-16 01:19:23.190] [puff::index::jointLog] [info] mphf size = 0.0125198 MB 2: [2026-04-16 01:19:23.190] [puff::index::jointLog] [info] chunk size = 9,796 2: [2026-04-16 01:19:23.190] [puff::index::jointLog] [info] chunk 0 = [0, 9,796) 2: [2026-04-16 01:19:23.190] [puff::index::jointLog] [info] chunk 1 = [9,796, 19,562) 2: [2026-04-16 01:19:23.192] [puff::index::jointLog] [info] finished populating pos vector 2: [2026-04-16 01:19:23.192] [puff::index::jointLog] [info] writing index components 2: [2026-04-16 01:19:23.192] [puff::index::jointLog] [info] finished writing dense pufferfish index 2: [2026-04-16 01:19:23.193] [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: [2026-04-16 01:19:23.231] [jointLog] [info] setting maxHashResizeThreads to 42 2: ----------------------------------------- 2: | Loading contig table | Time = 33.683 us 2: ----------------------------------------- 2: size = 24 2: ----------------------------------------- 2: | Loading contig offsets | Time = 93.853 us 2: ----------------------------------------- 2: ----------------------------------------- 2: | Loading reference lengths | Time = 10.156 us 2: ----------------------------------------- 2: ----------------------------------------- 2: | Loading mphf table | Time = 63.932 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 = 143.57 us 2: ----------------------------------------- 2: size = 19592 2: ----------------------------------------- 2: | Loading sequence | Time = 88.154 us 2: ----------------------------------------- 2: size = 18902 2: ----------------------------------------- 2: | Loading positions | Time = 117.14 us 2: ----------------------------------------- 2: size = 28562 2: ----------------------------------------- 2: | Loading reference sequence | Time = 74.993 us 2: ----------------------------------------- 2: ----------------------------------------- 2: | Loading reference accumulative lengths | Time = 9.24 us 2: ----------------------------------------- 2: [2026-04-16 01:19:23.231] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. 2: [2026-04-16 01:19:23.231] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 2: [2026-04-16 01:19:23.232] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35. 2: [2026-04-16 01:19:23.232] [jointLog] [info] parsing read library format 2: [2026-04-16 01:19:23.232] [jointLog] [info] There is 1 library. 2: [2026-04-16 01:19:23.232] [jointLog] [info] Loading pufferfish index 2: [2026-04-16 01:19:23.232] [jointLog] [info] Loading dense pufferfish index. 2: [2026-04-16 01:19:23.233] [jointLog] [info] done 2: [2026-04-16 01:19:23.289] [jointLog] [info] Index contained 15 targets 2: [2026-04-16 01:19:23.289] [jointLog] [info] Number of decoys : 0 2: 2: 2: 2: 2: 2: 2: 2: 2: 2: 2: 2: 2: [2026-04-16 01:19:23.509] [jointLog] [info] Computed 28 rich equivalence classes for further processing 2: [2026-04-16 01:19:23.509] [jointLog] [info] Counted 10,000 total reads in the equivalence classes 2: [2026-04-16 01:19:23.523] [jointLog] [info] Number of mappings discarded because of alignment score : 67 2: [2026-04-16 01:19:23.523] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0 2: [2026-04-16 01:19:23.523] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 2: [2026-04-16 01:19:23.523] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0 2: [2026-04-16 01:19:23.523] [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: [2026-04-16 01:19:23.523] [jointLog] [info] Mapping rate = 100% 2: 2: [2026-04-16 01:19:23.523] [jointLog] [info] finished quantifyLibrary() 2: [2026-04-16 01:19:23.523] [jointLog] [info] Starting optimizer 2: [2026-04-16 01:19:23.524] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate 2: [2026-04-16 01:19:23.524] [jointLog] [info] iteration = 0 | max rel diff. = 14.87 2: [2026-04-16 01:19:23.525] [jointLog] [info] iteration = 100 | max rel diff. = 3.90117e-05 2: [2026-04-16 01:19:23.525] [jointLog] [info] Finished optimizer 2: [2026-04-16 01:19:23.525] [jointLog] [info] writing output 2: 2: Salmon (read) ran successfully 2/2 Test #2: salmon_read_test_quasi ........... Passed 0.92 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 1.14 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 -j42 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/ntcard/ntcard-targets-release.cmake' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets.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/twopaco/twopaco-targets.cmake' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake' removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco' 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/graphdump/graphdump-targets-release.cmake' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets.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/libtwopaco.a' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libsalmon_core.a' 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/themetoggle.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/search-focus.js 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_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/642106 and its subdirectories I: Current time: Thu Apr 16 01:19:56 -12 2026 I: pbuilder-time-stamp: 1776345596 Fri Mar 14 06:56:58 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Fri Mar 14 06:56:58 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Fri Mar 14 07:49:44 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Fri Mar 14 07:49:44 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 Changed-By: Michael R. Crusoe 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: c30bd99b30cb592edb14111720f01b066776fd94 43079268 salmon-dbgsym_1.10.2+ds1-1_amd64.deb 0395c65c678d7d172e93e81518ba52b28eaa2794 11675 salmon_1.10.2+ds1-1_amd64.buildinfo bcecc3e1b5e347c196e1c16098cecf9adef8e780 3422348 salmon_1.10.2+ds1-1_amd64.deb Checksums-Sha256: 04b5afd8a4332c894f1b59ae348863ab9544ba7980006863bec91dacadc23624 43079268 salmon-dbgsym_1.10.2+ds1-1_amd64.deb a80b143372b2fd8464b61d478bbbe409dacea46a5472791d603bf7da148ad86f 11675 salmon_1.10.2+ds1-1_amd64.buildinfo ae9c4b367e1b5514180a61b5ec529081fd1f5e0015d8b870418877d4269638c0 3422348 salmon_1.10.2+ds1-1_amd64.deb Files: 12248292ee55323618711a4f1fffc7ff 43079268 debug optional salmon-dbgsym_1.10.2+ds1-1_amd64.deb 62a0913b58d7c37de1fc381dbeb69f45 11675 science optional salmon_1.10.2+ds1-1_amd64.buildinfo 68a1d638cd8e30e8b693545206803672 3422348 science optional salmon_1.10.2+ds1-1_amd64.deb Fri Mar 14 07:49:46 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_6-35333.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.wHaKwDZB/salmon_1.10.2+ds1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.wHaKwDZB/salmon_1.10.2+ds1-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.wHaKwDZB/salmon_1.10.2+ds1-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.wHaKwDZB/b1/salmon_1.10.2+ds1-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.wHaKwDZB/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: 0.680s) 0.430s 6 calls xz 0.094s 6 calls diff 0.078s 2 calls cmp 0.078s 2 calls cmp (external) 0.001s 14 calls cmp (internal) ## compare_files (cumulative) (total time: 2.686s) 0.866s 1 call abc.DotChangesFile 0.762s 1 call abc.DebFile 0.721s 2 calls abc.XzFile 0.234s 1 call abc.DebDataTarFile 0.072s 1 call abc.TextFile 0.026s 1 call abc.TarFile 0.006s 1 call abc.Md5sumsFile ## container_extract (total time: 0.514s) 0.430s 6 calls diffoscope.comparators.xz.XzContainer 0.067s 98 calls diffoscope.comparators.deb.DebTarContainer 0.015s 8 calls diffoscope.comparators.deb.DebContainer 0.002s 6 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.285s) 0.285s 48 calls linediff ## has_same_content_as (total time: 0.080s) 0.059s 2 calls abc.DebFile 0.019s 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: 46.253s) 46.252s 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: 44.671s) 44.668s 1 call html 0.002s 1 call text 0.001s 1 call json ## recognizes (total time: 0.514s) 0.406s 12 calls diffoscope.comparators.binary.FilesystemFile 0.052s 546 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.034s 108 calls diffoscope.comparators.debian.DebControlMember 0.021s 260 calls diffoscope.comparators.utils.archive.ArchiveMember ## specialize (total time: 0.809s) 0.809s 16 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 46.553s CPU time consumed: 46.654s Fri Mar 14 07:50:34 UTC 2025 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Fri Mar 14 07:50:34 UTC 2025 E: salmon failed to build reproducibly in trixie on amd64. Fri Mar 14 07:50:36 UTC 2025 I: Submitting .buildinfo files to external archives: Fri Mar 14 07:50:36 UTC 2025 I: Submitting 16K b1/salmon_1.10.2+ds1-1_amd64.buildinfo.asc Fri Mar 14 07:50:37 UTC 2025 I: Submitting 16K b2/salmon_1.10.2+ds1-1_amd64.buildinfo.asc Fri Mar 14 07:50:38 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Mar 14 07:50:38 UTC 2025 I: Done submitting .buildinfo files. Fri Mar 14 07:50:38 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'