Sun Jan 26 01:48:19 UTC 2025 I: starting to build salmon/trixie/arm64 on jenkins on '2025-01-26 01:47' Sun Jan 26 01:48:19 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_1/57399/console.log Sun Jan 26 01:48:19 UTC 2025 I: Downloading source for trixie/salmon=1.10.2+ds1-1 --2025-01-26 01:48:19-- 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% 386M=0s 2025-01-26 01:48:19 (386 MB/s) - ‘salmon_1.10.2+ds1-1.dsc’ saved [2558/2558] Sun Jan 26 01:48:19 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----- Sun Jan 26 01:48:19 UTC 2025 I: Checking whether the package is not for us Sun Jan 26 01:48:19 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Sun Jan 26 01:48:19 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Sun Jan 26 01:53:28 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Feb 27 20:11:21 -12 2026 I: pbuilder-time-stamp: 1772266281 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/3136144/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='52e707c602364165ad97ea0051851686' 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='3136144' 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.bMU0zDvN/pbuilderrc_o3Cc --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.bMU0zDvN/b1 --logfile b1/build.log salmon_1.10.2+ds1-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3136144/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: arm64 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 ... 19970 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} fonts-mathjax{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} 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-mathjax{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} libnsl2{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} libpython3.12-minimal{a} libpython3.12-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} libtirpc-common{a} libtirpc3t64{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} 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-autocommand{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-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{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-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3.12{a} python3.12-doc{a} python3.12-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 psmisc publicsuffix python3-pil wget 0 packages upgraded, 226 newly installed, 0 to remove and 0 not upgraded. Need to get 137 MB of archives. After unpacking 750 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 fonts-lato all 2.015-1 [2780 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.8-5 [810 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.8-5 [1934 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.12.8-1 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024b-6 [257 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 15 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.8-5 [1904 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.8-5 [677 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.12.8-1 [9788 B] Get: 25 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.12.8-1 [27.9 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.4.0-2 [1385 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20241223 [164 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-4 [198 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-4 [723 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 cmake-data all 3.31.4-2 [2267 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.11.1-1+b1 [324 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 cmake arm64 3.31.4-2 [9898 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 comerr-dev arm64 2.1-1.47.2-1 [55.9 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 75 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-4 [1532 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 docutils-doc all 0.21.2+dfsg-2 [1122 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 icu-devtools arm64 72.1-6 [196 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libboost1.83-dev arm64 1.83.0-4 [10.6 MB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libboost-atomic1.83.0 arm64 1.83.0-4 [233 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libboost-atomic1.83-dev arm64 1.83.0-4 [234 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libboost-chrono1.83.0t64 arm64 1.83.0-4 [239 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libboost-chrono1.83-dev arm64 1.83.0-4 [245 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libboost-date-time1.83.0 arm64 1.83.0-4 [231 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libboost-serialization1.83.0 arm64 1.83.0-4 [325 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libboost-serialization1.83-dev arm64 1.83.0-4 [375 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libboost-date-time1.83-dev arm64 1.83.0-4 [239 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libboost-filesystem1.83.0 arm64 1.83.0-4 [273 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libboost-system1.83.0 arm64 1.83.0-4 [231 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libboost-system1.83-dev arm64 1.83.0-4 [231 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libboost-filesystem1.83-dev arm64 1.83.0-4 [293 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libboost-filesystem-dev arm64 1.83.0.2+b2 [3616 B] Get: 107 http://deb.debian.org/debian trixie/main arm64 libboost-regex1.83.0 arm64 1.83.0-4 [314 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libicu-dev arm64 72.1-6 [10.3 MB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libboost-regex1.83-dev arm64 1.83.0-4 [338 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libboost-iostreams1.83-dev arm64 1.83.0-4 [261 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libboost-iostreams-dev arm64 1.83.0.2+b2 [3568 B] Get: 112 http://deb.debian.org/debian trixie/main arm64 libboost-program-options1.83.0 arm64 1.83.0-4 [331 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libboost-program-options1.83-dev arm64 1.83.0-4 [371 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libboost-program-options-dev arm64 1.83.0.2+b2 [3600 B] Get: 115 http://deb.debian.org/debian trixie/main arm64 libboost-system-dev arm64 1.83.0.2+b2 [3720 B] Get: 116 http://deb.debian.org/debian trixie/main arm64 libboost-thread1.83.0 arm64 1.83.0-4 [265 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libboost-thread1.83-dev arm64 1.83.0-4 [277 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libboost-thread-dev arm64 1.83.0.2+b2 [3616 B] Get: 119 http://deb.debian.org/debian trixie/main arm64 libboost-timer1.83.0 arm64 1.83.0-4 [235 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libboost-timer1.83-dev arm64 1.83.0-4 [236 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libboost-timer-dev arm64 1.83.0.2+b2 [3712 B] Get: 122 http://deb.debian.org/debian trixie/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libbwa-dev arm64 0.7.18-1 [151 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 rapidjson-dev all 1.1.0+dfsg2-7.3 [98.0 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libcereal-dev arm64 1.3.2+dfsg-5 [221 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.11.1-1+b1 [331 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libunbound8 arm64 1.22.0-1 [553 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libldap-dev arm64 2.6.9+dfsg-1 [305 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 libnghttp3-dev arm64 1.6.0-2 [86.5 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.9.1-1 [23.0 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 libngtcp2-dev arm64 1.9.1-1 [162 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 libssl-dev arm64 3.4.0-2 [3234 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 libzstd-dev arm64 1.5.6+dfsg-2 [329 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.11.1-1+b1 [461 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 libdivsufsort3 arm64 2.0.1-6+b1 [39.9 kB] Get: 159 http://deb.debian.org/debian trixie/main arm64 libdivsufsort-dev arm64 2.0.1-6+b1 [19.1 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-4 [14.0 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 libfmt10 arm64 10.1.1+ds1-4 [121 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 libfmt-dev arm64 10.1.1+ds1-4 [177 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 libgff-dev arm64 2.0.0-3 [146 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 libhtscodecs-dev arm64 1.6.1-1 [2979 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 libhwloc15 arm64 2.11.2-1 [141 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 libjellyfish-2.0-2 arm64 2.3.1-4 [61.6 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 libjellyfish-2.0-dev arm64 2.3.1-4 [135 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 libjemalloc2 arm64 5.3.0-2+b2 [217 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 libjemalloc-dev arm64 5.3.0-2+b2 [357 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 177 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 libpthread-stubs0-dev arm64 0.5-1 [5164 B] Get: 179 http://deb.debian.org/debian trixie/main arm64 libsimde-dev all 0.8.2-2 [467 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 libspdlog1.15 arm64 1:1.15.0+ds-2+b1 [98.9 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 libspdlog-dev arm64 1:1.15.0+ds-2+b1 [89.6 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 libstaden-read14t64 arm64 1.15.0-1.1+b2 [252 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 libstaden-read-dev arm64 1.15.0-1.1+b2 [334 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 libtbbmalloc2 arm64 2022.0.0-1 [35.6 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 libtbbbind-2-5 arm64 2022.0.0-1 [14.3 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 libtbb12 arm64 2022.0.0-1 [66.5 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 libtbb-dev arm64 2022.0.0-1 [199 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 libtclap-dev arm64 1.2.5-1+b1 [3359 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 python-requests-doc all 2.32.3+dfsg-1 [196 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 197 http://deb.debian.org/debian trixie/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 199 http://deb.debian.org/debian trixie/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 200 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 201 http://deb.debian.org/debian trixie/main arm64 python3-babel all 2.16.0-1 [114 kB] Get: 202 http://deb.debian.org/debian trixie/main arm64 python3-certifi all 2024.12.14+ds-1 [9624 B] Get: 203 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 204 http://deb.debian.org/debian trixie/main arm64 python3-charset-normalizer arm64 3.4.0-1+b1 [129 kB] Get: 205 http://deb.debian.org/debian trixie/main arm64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 206 http://deb.debian.org/debian trixie/main arm64 python3.12-doc all 3.12.8-5 [13.2 MB] Get: 207 http://deb.debian.org/debian trixie/main arm64 python3-doc all 3.12.8-1 [9992 B] Get: 208 http://deb.debian.org/debian trixie/main arm64 python3-docs-theme all 2024.10-1 [19.0 kB] Get: 209 http://deb.debian.org/debian trixie/main arm64 python3-roman all 4.2-1 [10.4 kB] Get: 210 http://deb.debian.org/debian trixie/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 211 http://deb.debian.org/debian trixie/main arm64 python3-idna all 3.8-2 [41.6 kB] Get: 212 http://deb.debian.org/debian trixie/main arm64 python3-imagesize all 1.4.1-1 [6688 B] Get: 213 http://deb.debian.org/debian trixie/main arm64 python3-markupsafe arm64 2.1.5-1+b3 [14.0 kB] Get: 214 http://deb.debian.org/debian trixie/main arm64 python3-jinja2 all 3.1.3-2 [120 kB] Get: 215 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.2-1 [55.3 kB] Get: 216 http://deb.debian.org/debian trixie/main arm64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 217 http://deb.debian.org/debian trixie/main arm64 python3-urllib3 all 2.3.0-1 [114 kB] Get: 218 http://deb.debian.org/debian trixie/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 219 http://deb.debian.org/debian trixie/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 220 http://deb.debian.org/debian trixie/main arm64 sphinx-common all 8.1.3-4 [616 kB] Get: 221 http://deb.debian.org/debian trixie/main arm64 python3-sphinx all 8.1.3-4 [468 kB] Get: 222 http://deb.debian.org/debian trixie/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-1 [1023 kB] Get: 223 http://deb.debian.org/debian trixie/main arm64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 224 http://deb.debian.org/debian trixie/main arm64 python3-sphinx-rtd-theme all 3.0.2+dfsg-1 [29.5 kB] Get: 225 http://deb.debian.org/debian trixie/main arm64 rapmap-dev all 0.15.0+dfsg-4 [193 kB] Get: 226 http://deb.debian.org/debian trixie/main arm64 sphinx-doc all 8.1.3-4 [3487 kB] Fetched 137 MB in 1s (226 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 ... 19970 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_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../16-libpython3.12-stdlib_3.12.8-5_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.8-5) ... Selecting previously unselected package python3.12. Preparing to unpack .../17-python3.12_3.12.8-5_arm64.deb ... Unpacking python3.12 (3.12.8-5) ... 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Setting up libhtscodecs2:arm64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libsimde-dev (0.8.2-2) ... Setting up libtbbmalloc2:arm64 (2022.0.0-1) ... Setting up libboost-program-options1.83.0:arm64 (1.83.0-4) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libboost1.83-dev:arm64 (1.83.0-4) ... Setting up fonts-lato (2.015-1) ... Setting up fonts-mathjax (2.7.9+dfsg-1) ... Setting up libicu72:arm64 (72.1-6) ... Setting up docutils-doc (0.21.2+dfsg-2) ... Setting up libzstd-dev:arm64 (1.5.6+dfsg-2) ... Setting up bsdextrautils (2.40.4-1) ... Setting up libjs-mathjax (2.7.9+dfsg-1) ... Setting up libboost-date-time1.83.0:arm64 (1.83.0-4) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libboost-timer1.83.0:arm64 (1.83.0-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libboost-regex1.83.0:arm64 (1.83.0-4) ... Setting up libdebhelper-perl (13.23) ... 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Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-8+b1) ... Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Feb 28 08:11:56 UTC 2026. Universal Time is now: Sat Feb 28 08:11:56 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-4) ... Setting up libjellyfish-2.0-2:arm64 (2.3.1-4) ... Setting up libboost-serialization1.83.0:arm64 (1.83.0-4) ... Setting up libjemalloc-dev (5.3.0-2+b2) ... Setting up libhtscodecs-dev:arm64 (1.6.1-1) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:arm64 (1.22.0-1) ... Setting up libpkgconf3:arm64 (1.8.1-4) ... Setting up libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3) ... Setting up libgff-dev (2.0.0-3) ... Setting up libboost-program-options-dev:arm64 (1.83.0.2+b2) ... Setting up libboost-chrono1.83.0t64:arm64 (1.83.0-4) ... Setting up libjsoncpp26:arm64 (1.9.6-3) ... Setting up libproc2-0:arm64 (2:4.0.4-6) ... 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Setting up libngtcp2-dev:arm64 (1.9.1-1) ... Setting up pkgconf:arm64 (1.8.1-4) ... Setting up libtbbbind-2-5:arm64 (2022.0.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3+b1) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libboost-timer1.83-dev:arm64 (1.83.0-4) ... Setting up libboost-date-time1.83-dev:arm64 (1.83.0-4) ... Setting up libldap-dev:arm64 (2.6.9+dfsg-1) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libeigen3-dev (3.4.0-4) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libfmt-dev:arm64 (10.1.1+ds1-4) ... Setting up libboost-regex1.83-dev:arm64 (1.83.0-4) ... Setting up pkg-config:arm64 (1.8.1-4) ... Setting up libspdlog1.15:arm64 (1:1.15.0+ds-2+b1) ... Setting up libssh2-1-dev:arm64 (1.11.1-1) ... Setting up libidn2-dev:arm64 (2.3.7-2+b1) ... Setting up libjs-sphinxdoc (8.1.3-4) ... 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Setting up python3-urllib3 (2.3.0-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.6.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-docs-theme (2024.10-1) ... Setting up libcurl4-gnutls-dev:arm64 (8.11.1-1+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up libstaden-read-dev (1.15.0-1.1+b2) ... Processing triggers for libc-bin (2.40-5) ... 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 (8.1.3-4) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-rtd-theme (3.0.2+dfsg-1) ... 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 arm64 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-aarch64-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/aarch64-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 64-bit ARM host. Setting USE_ARM to true. 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/aarch64-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 "5.6.3") 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/aarch64-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/aarch64-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/aarch64-linux-gnu/libcurl.so (found version "8.11.1") -- Found libstadenio: /usr/lib/aarch64-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/aarch64-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 (5.8s) -- 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-aarch64-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-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/salmon-1.10.2+ds1 -B/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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-aarch64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/DependInfo.cmake "--color=" make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu' cd 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/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common/SignalHandler.cpp [ 6%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o [ 7%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o [ 8%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o [ 9%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o [ 10%] Building CXX object src/CMakeFiles/alevin_core.dir/edlib.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 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-Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -MF CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o.d -o CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/tests/UnitTests.cpp cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -MD -MT 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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 [ 12%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o [ 13%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 [ 14%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 [ 15%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -D__SSE4_1__ -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -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 [ 16%] 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-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -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 [ 17%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -MF CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o.d -o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SingleCellProtocols.cpp [ 17%] Building CXX object src/CMakeFiles/salmon_core.dir/backtrace.cc.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 [ 18%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/xxhash.c.o -MF CMakeFiles/salmon_core.dir/xxhash.c.o.d -o CMakeFiles/salmon_core.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/xxhash.c cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C cc1: warning: command-line option '-Wno-deprecated-copy' is valid for C++/ObjC++ but not for C [ 19%] 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-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_gg.c make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu' [ 19%] Built target ksw2pp_sse2 [ 20%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 [ 21%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -MF CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o.d -o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/EffectiveLengthStats.cpp [ 22%] 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-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -D__SSE4_1__ -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c [ 23%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 [ 24%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -MF CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o.d -o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/LibraryFormat.cpp [ 25%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -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 [ 26%] Linking CXX static library libntcard.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -E cmake_link_script CMakeFiles/ntcard.dir/link.txt --verbose=1 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 '< >' /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-aarch64-linux-gnu' [ 26%] Built target ntcard [ 26%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -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 [ 27%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 [ 28%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinOpts.hpp:5, from /build/reproducible-path/salmon-1.10.2+ds1/include/SingleCellProtocols.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/src/SingleCellProtocols.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /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 '< >' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 [ 29%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu' [ 30%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 [ 30%] Built target ksw2pp_sse4 [ 31%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 [ 32%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 [ 33%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu' [ 33%] Built target ksw2pp_basic 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-aarch64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu' [ 33%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o [ 34%] Linking CXX static library libksw2pp.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-14" qc libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o "/usr/bin/gcc-ranlib-14" libksw2pp.a [ 34%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 [ 34%] Built target ksw2pp [ 35%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 [ 36%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 [ 37%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonUtils.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/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/include/FastxParser.hpp:15, from /build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h: In instantiation of 'void moodycamel::details::swap_relaxed(std::atomic<_ITp>&, std::atomic<_ITp>&) [with T = std::thread::id]': /build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:3302:26: required from 'void moodycamel::ConcurrentQueue::ImplicitProducerKVP::swap(moodycamel::ConcurrentQueue::ImplicitProducerKVP&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' 3302 | details::swap_relaxed(key, other.key); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:3295:4: required from 'moodycamel::ConcurrentQueue::ImplicitProducerKVP& moodycamel::ConcurrentQueue::ImplicitProducerKVP::operator=(moodycamel::ConcurrentQueue::ImplicitProducerKVP&&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' 3295 | swap(other); | ^~~~ /usr/include/c++/14/bits/move.h:223:11: required from 'std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP; _Require<__not_<__is_tuple_like<_Tp> >, is_move_constructible<_Tp>, is_move_assignable<_Tp> > = void]' 223 | __a = _GLIBCXX_MOVE(__b); | ^ /usr/include/c++/14/bits/stl_algobase.h:185:11: required from 'void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*; _ForwardIterator2 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*]' 185 | swap(*__a, *__b); | ~~~~^~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:215:16: required from '_ForwardIterator2 std::swap_ranges(_ForwardIterator1, _ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*; _ForwardIterator2 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*]' 215 | std::iter_swap(__first1, __first2); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/array:127:25: required from 'void std::array<_Tp, _Nm>::swap(std::array<_Tp, _Nm>&) [with _Tp = moodycamel::ConcurrentQueue, std::default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP; long unsigned int _Nm = 32]' 127 | { std::swap_ranges(begin(), end(), __other.begin()); } | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:3343:43: required from 'void moodycamel::ConcurrentQueue::swap_implicit_producer_hashes(moodycamel::ConcurrentQueue&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' 3343 | initialImplicitProducerHashEntries.swap(other.initialImplicitProducerHashEntries); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:955:3: required from 'moodycamel::ConcurrentQueue& moodycamel::ConcurrentQueue::swap_internal(moodycamel::ConcurrentQueue&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' 955 | swap_implicit_producer_hashes(other); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:926:10: required from 'moodycamel::ConcurrentQueue& moodycamel::ConcurrentQueue::operator=(moodycamel::ConcurrentQueue&&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' 926 | return swap_internal(other); | ^~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp:43:14: required from 'fastx_parser::FastxParser::FastxParser(std::vector >, std::vector >, uint32_t, uint32_t, uint32_t) [with T = klibpp::KSeq; uint32_t = unsigned int]' 43 | readQueue_ = moodycamel::ConcurrentQueue>>( | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 44 | 4 * numConsumers, numParsers, 0); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp:425:16: required from here 425 | template class FastxParser; | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:509:19: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 509 | T temp = std::move(left.load(std::memory_order_relaxed)); | ^~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:509:19: note: remove 'std::move' call /build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:510:27: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 510 | left.store(std::move(right.load(std::memory_order_relaxed)), std::memory_order_relaxed); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:510:27: note: remove 'std::move' call [ 38%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 [ 39%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 [ 40%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -MF CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/DistributionUtils.cpp [ 41%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonExceptions.cpp 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 '< >' [ 42%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonStringUtils.cpp [ 43%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -MF CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o.d -o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SimplePosBias.cpp 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 '< >' [ 44%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 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 '< >' [ 45%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 [ 45%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 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 '< >' [ 45%] 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-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 [ 46%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 [ 47%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndex.cpp [ 48%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 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 '< >' 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 '< >' /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/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 '< >' 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 '< >' [ 48%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 [ 49%] Linking CXX static library libgraphdump.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu' [ 49%] Built target graphdump [ 50%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 [ 51%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 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 '< >' 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)); | ^~~~~~~~~~~~~~~~~~~~~~ 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 '< >' [ 52%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o -MF CMakeFiles/puffer.dir/rank9sel.cpp.o.d -o CMakeFiles/puffer.dir/rank9sel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/rank9sel.cpp [ 53%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o -MF CMakeFiles/puffer.dir/rank9b.cpp.o.d -o CMakeFiles/puffer.dir/rank9b.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/rank9b.cpp 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); | ^~~~~~~~~~~~~~~~~~~~~~ [ 54%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -MF CMakeFiles/puffer.dir/PufferfishValidate.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishValidate.cpp [ 55%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o -MF CMakeFiles/puffer.dir/PufferfishStats.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishStats.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishStats.cpp /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/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 '< >' [ 56%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -MF CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishTestLookup.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishStats.cpp:16: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /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 '< >' /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) { | ~~~~~~~~~^ [ 56%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -MF CMakeFiles/puffer.dir/PufferfishExamine.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishExamine.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/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 '< >' [ 57%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -MF CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishKmerQuery.cpp [ 58%] Linking CXX static library libalevin_core.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 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 '< >' "/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-aarch64-linux-gnu' [ 58%] Built target alevin_core [ 59%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o -MF CMakeFiles/puffer.dir/FastxParser.cpp.o.d -o CMakeFiles/puffer.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FastxParser.cpp [ 60%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp [ 61%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o -MF CMakeFiles/puffer.dir/PufferFS.cpp.o.d -o CMakeFiles/puffer.dir/PufferFS.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferFS.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/FastxParser.hpp:15, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FastxParser.cpp:1: /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/concurrentqueue.h: In instantiation of 'void moodycamel::details::swap_relaxed(std::atomic<_ITp>&, std::atomic<_ITp>&) [with T = std::thread::id]': /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/concurrentqueue.h:3302:26: required from 'void moodycamel::ConcurrentQueue::ImplicitProducerKVP::swap(moodycamel::ConcurrentQueue::ImplicitProducerKVP&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' 3302 | details::swap_relaxed(key, other.key); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/concurrentqueue.h:3295:4: required from 'moodycamel::ConcurrentQueue::ImplicitProducerKVP& moodycamel::ConcurrentQueue::ImplicitProducerKVP::operator=(moodycamel::ConcurrentQueue::ImplicitProducerKVP&&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' 3295 | swap(other); | ^~~~ /usr/include/c++/14/bits/move.h:223:11: required from 'std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP; _Require<__not_<__is_tuple_like<_Tp> >, is_move_constructible<_Tp>, is_move_assignable<_Tp> > = void]' 223 | __a = _GLIBCXX_MOVE(__b); | ^ /usr/include/c++/14/bits/stl_algobase.h:185:11: required from 'void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*; _ForwardIterator2 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*]' 185 | swap(*__a, *__b); | ~~~~^~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:215:16: required from '_ForwardIterator2 std::swap_ranges(_ForwardIterator1, _ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*; _ForwardIterator2 = moodycamel::ConcurrentQueue, default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*]' 215 | std::iter_swap(__first1, __first2); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/array:127:25: required from 'void std::array<_Tp, _Nm>::swap(std::array<_Tp, _Nm>&) [with _Tp = moodycamel::ConcurrentQueue, std::default_delete > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP; long unsigned int _Nm = 32]' 127 | { std::swap_ranges(begin(), end(), __other.begin()); } | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/concurrentqueue.h:3343:43: required from 'void moodycamel::ConcurrentQueue::swap_implicit_producer_hashes(moodycamel::ConcurrentQueue&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' 3343 | initialImplicitProducerHashEntries.swap(other.initialImplicitProducerHashEntries); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/concurrentqueue.h:955:3: required from 'moodycamel::ConcurrentQueue& moodycamel::ConcurrentQueue::swap_internal(moodycamel::ConcurrentQueue&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' 955 | swap_implicit_producer_hashes(other); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/concurrentqueue.h:926:10: required from 'moodycamel::ConcurrentQueue& moodycamel::ConcurrentQueue::operator=(moodycamel::ConcurrentQueue&&) [with T = std::unique_ptr, std::default_delete > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]' 926 | return swap_internal(other); | ^~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FastxParser.cpp:43:14: required from 'fastx_parser::FastxParser::FastxParser(std::vector >, std::vector >, uint32_t, uint32_t, uint32_t) [with T = klibpp::KSeq; uint32_t = unsigned int]' 43 | readQueue_ = moodycamel::ConcurrentQueue>>( | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 44 | 4 * numConsumers, numParsers, 0); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FastxParser.cpp:425:16: required from here 425 | template class FastxParser; | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/concurrentqueue.h:509:19: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 509 | T temp = std::move(left.load(std::memory_order_relaxed)); | ^~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/concurrentqueue.h:509:19: note: remove 'std::move' call /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/concurrentqueue.h:510:27: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 510 | left.store(std::move(right.load(std::memory_order_relaxed)), std::memory_order_relaxed); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/concurrentqueue.h:510:27: note: remove 'std::move' call [ 62%] Building C object external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o -MF CMakeFiles/puffer.dir/xxhash.c.o.d -o CMakeFiles/puffer.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/xxhash.c cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C [ 63%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o -MF CMakeFiles/puffer.dir/FixFasta.cpp.o.d -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/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 '< >' [ 64%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 [ 65%] Linking CXX static library libsalmon_core.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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-aarch64-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-aarch64-linux-gnu' [ 65%] Built target salmon_core 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 '< >' [ 65%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o -MF CMakeFiles/puffer.dir/MemChainer.cpp.o.d -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemChainer.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/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)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 66%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o -MF CMakeFiles/puffer.dir/PuffAligner.cpp.o.d -o CMakeFiles/puffer.dir/PuffAligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PuffAligner.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/Util.hpp:19, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishIndex.hpp:12, from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/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 '< >' [ 67%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -MF CMakeFiles/puffer.dir/PufferfishAligner.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishAligner.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/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/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/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 '< >' [ 68%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -MF CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o.d -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/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 '< >' [ 69%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -MF CMakeFiles/puffer.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/metro/metrohash64.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/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)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 [ 71%] Linking CXX static library libUnitTestsMain.a cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/UnitTestsMain.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/UnitTestsMain.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-aarch64-linux-gnu' [ 71%] 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-aarch64-linux-gnu' cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/unitTests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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-aarch64-linux-gnu' [ 72%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o [ 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-aarch64-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 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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-aarch64-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 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -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 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o -MF CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o.d -o CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/tests/GCSampleTests.cpp [ 75%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -MF CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o.d -o CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/tests/LibraryTypeTests.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/spdlog_impl.h:12, from /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/spdlog.h:192, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonOpts.hpp:7, from /build/reproducible-path/salmon-1.10.2+ds1/include/SalmonUtils.hpp:30, from /build/reproducible-path/salmon-1.10.2+ds1/tests/LibraryTypeTests.cpp:6: /build/reproducible-path/salmon-1.10.2+ds1/include/spdlog/details/../details/registry.h:197:22: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 197 | registry_t() {} | ^ /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 '< >' 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++; | ^~~~ 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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:105:31, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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++; | ^~~~ 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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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 'fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)::' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:107:26, inlined from 'bool fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)' at /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /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 fixFasta(single_parser*, spp::sparse_hash_set >&, bool, uint32_t, std::string&, bool, bool, std::mutex&, std::shared_ptr, std::string, std::vector&, std::vector, short unsigned int> >&)': /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++; | ^~~~ [ 76%] Linking CXX executable unitTests cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -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 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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-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o -MF CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o.d -o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/BuildSalmonIndex.cpp cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/Graph.cpp.o -MF CMakeFiles/salmon.dir/Graph.cpp.o.d -o CMakeFiles/salmon.dir/Graph.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/Graph.cpp [ 86%] Building CXX object src/CMakeFiles/salmon.dir/Alevin.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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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/AlevinHash.cpp.o -MF CMakeFiles/salmon.dir/AlevinHash.cpp.o.d -o CMakeFiles/salmon.dir/AlevinHash.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinHash.cpp [ 87%] Building CXX object src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -MF CMakeFiles/salmon.dir/SalmonAlevin.cpp.o.d -o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp [ 88%] Building CXX object src/CMakeFiles/salmon.dir/WhiteList.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/WhiteList.cpp.o -MF CMakeFiles/salmon.dir/WhiteList.cpp.o.d -o CMakeFiles/salmon.dir/WhiteList.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/WhiteList.cpp 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/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/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/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/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/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/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/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/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 '< >' [ 89%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantify.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantify.cpp 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/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)); | ^~~~~~~~~~~~~~~~~~~~~~ [ 90%] Building CXX object src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp 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){ | ^~~~~~~~~~~ | & 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/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); | ^~~~~~~~~~~~~~~~~~~~~~ [ 91%] Building CXX object src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -MF CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o.d -o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentStartPositionDistribution.cpp [ 92%] Building CXX object src/CMakeFiles/salmon.dir/GZipWriter.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 /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, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 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/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/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 = 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::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, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /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/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 = 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/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/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/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, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 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::_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; 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 = 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::_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/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/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/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, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 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/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/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/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, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~ /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/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/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/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::_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, 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::_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/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/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)); | ^~~~~~~~~~~~~~~~~~~~~~ /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/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/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/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 = 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/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/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/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/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)); | ^~~~~~~~~~~~~~~~~~~~~~ /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/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/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/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::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/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/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/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/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)); | ^~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~ 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 '< >' [ 93%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantMerge.cpp [ 94%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 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 '< >' /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)); | ^~~~~~~~~~~~~~~~~~~~~~ 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/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 '< >' [ 94%] Building CXX object src/CMakeFiles/salmon.dir/FASTAParser.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 [ 95%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 [ 96%] Building CXX object src/CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 [ 97%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -MF CMakeFiles/salmon.dir/AlignmentCommon.cpp.o.d -o CMakeFiles/salmon.dir/AlignmentCommon.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlignmentCommon.cpp In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/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); | ^~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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 /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/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/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/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/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 '< >' [ 99%] Building CXX object src/CMakeFiles/salmon.dir/BAMUtils.cpp.o cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -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/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::_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/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, | ~~~~~~~~~~~~~~~~^~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In constructor 'ONTAlignmentModel::ONTAlignmentModel(double, uint32_t)': /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:17:45: warning: unused parameter 'alpha' [-Wunused-parameter] 17 | ONTAlignmentModel::ONTAlignmentModel(double alpha, uint32_t readBins) | ~~~~~~~^~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function 'double ONTAlignmentModel::logLikelihood(const UnpairedRead&, const UnpairedRead&, Transcript&)': /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:53:22: warning: comparison of integer expressions of different signedness: 'int32_t' {aka 'int'} and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] 53 | if(counts.sclips() >= cigarRLen) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function 'void ONTAlignmentModel::update(const UnpairedRead&, const UnpairedRead&, Transcript&, double, double)': /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:137:56: warning: unused parameter 'p' [-Wunused-parameter] 137 | Transcript& ref, double p, double mass) { | ~~~~~~~^ /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp: In member function 'void ONTAlignmentModel::printModel(std::ostream&)': /build/reproducible-path/salmon-1.10.2+ds1/src/ONTAlignmentModel.cpp:194:50: warning: unused parameter 'os' [-Wunused-parameter] 194 | void ONTAlignmentModel::printModel(std::ostream& os) { | ~~~~~~~~~~~~~~^~ In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/EquivalenceClassBuilder.hpp:18, from /build/reproducible-path/salmon-1.10.2+ds1/include/AlignmentLibrary.hpp:19: /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_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)); | ^~~~~~~~~~~~~~~~~~~~~~ [100%] Linking CXX executable salmon cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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 -mbranch-protection=standard -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/aarch64-linux-gnu/libcurl.so -lz -lm /usr/lib/aarch64-linux-gnu/libstaden-read.so /usr/lib/aarch64-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-aarch64-linux-gnu' [100%] Built target salmon make[3]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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". 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[ref.footnote] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/salmon.rst:2: WARNING: Duplicate explicit target name: "here". [docutils] /build/reproducible-path/salmon-1.10.2+ds1/doc/source/salmon.rst:2: WARNING: Duplicate explicit target name: "here". [docutils] looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/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/sidebar.js Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/classic.css Writing evaluated template result to /build/reproducible-path/salmon-1.10.2+ds1/doc/build/html/_static/sidebar.js copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 17%] alevin writing output... [ 33%] building writing output... [ 50%] file_formats writing output... [ 67%] index writing output... [ 83%] library_type writing output... [100%] salmon generating indices... genindex done writing additional pages... search done copying images... [100%] ReadLibraryIllustration.png dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 33 warnings. The HTML pages are in doc/build/html. mv doc/license.rst doc/source/ cd obj*/src && \ help2man --no-discard-stderr --no-info --name="highly-accurate, transcript-level quantification estimates from RNA-seq data"\ ./salmon > ../../debian/salmon.1 && \ for option in index quant swim; do help2man --no-discard-stderr \ --version-string="1.10.2+ds1" --no-info "./salmon --no-version-check ${option}" \ --include=../../debian/salmon-${option}-man-include \ > ../../debian/salmon-${option}.1; done make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1' dh_auto_test --no-parallel cd obj-aarch64-linux-gnu && make -j1 test ARGS\+=--verbose ARGS\+=-j1 make[2]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j1 UpdateCTestConfiguration from :/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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-aarch64-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 (2001374 assertions in 4 test cases) 1: 1/2 Test #1: unit_tests ....................... Passed 0.26 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-aarch64-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: [2026-02-27 20:15:50.674] [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: [2026-02-27 20:15:50.674] [jLog] [info] building index 2: out : sample_salmon_quasi_index 2: [2026-02-27 20:15:50.675] [puff::index::jointLog] [info] Running fixFasta 2: 2: [Step 1 of 4] : counting k-mers 2: 2: [2026-02-27 20:15:50.680] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides 2: [2026-02-27 20:15:50.680] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts 2: wrote 15 cleaned references 2: [2026-02-27 20:15:50.681] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers 2: [2026-02-27 20:15:50.682] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20 2: Threads = 2 2: Vertex length = 31 2: Hash functions = 5 2: Filter size = 1048576 2: Capacity = 2 2: Files: 2: sample_salmon_quasi_index/ref_k31_fixed.fa 2: -------------------------------------------------------------------------------- 2: Round 0, 0:1048576 2: Pass Filling Filtering 2: 1 0 0 2: 2 0 0 2: True junctions count = 14 2: False junctions count = 18 2: Hash table size = 32 2: Candidate marks count = 55 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: [2026-02-27 20:15:50.720] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file. 2: [2026-02-27 20:15:50.720] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory sample_salmon_quasi_index 2: size = 19592 2: ----------------------------------------- 2: | Loading contigs | Time = 101.84 us 2: ----------------------------------------- 2: size = 19592 2: ----------------------------------------- 2: | Loading contig boundaries | Time = 44.08 us 2: ----------------------------------------- 2: Number of ones: 23 2: Number of ones per inventory item: 512 2: Inventory entries filled: 1 2: 23 2: [2026-02-27 20:15:50.720] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure. 2: [2026-02-27 20:15:50.720] [puff::index::jointLog] [info] contig count for validation: 23 2: [2026-02-27 20:15:50.720] [puff::index::jointLog] [info] Total # of Contigs : 23 2: [2026-02-27 20:15:50.720] [puff::index::jointLog] [info] Total # of numerical Contigs : 23 2: [2026-02-27 20:15:50.720] [puff::index::jointLog] [info] Total # of contig vec entries: 36 2: [2026-02-27 20:15:50.720] [puff::index::jointLog] [info] bits per offset entry 6 2: [2026-02-27 20:15:50.720] [puff::index::jointLog] [info] Done constructing the contig vector. 24 2: [2026-02-27 20:15:50.720] [puff::index::jointLog] [info] # segments = 23 2: [2026-02-27 20:15:50.720] [puff::index::jointLog] [info] total length = 19,592 2: [2026-02-27 20:15:50.720] [puff::index::jointLog] [info] Reading the reference files ... 2: [2026-02-27 20:15:50.722] [puff::index::jointLog] [info] positional integer width = 15 2: [2026-02-27 20:15:50.722] [puff::index::jointLog] [info] seqSize = 19,592 2: [2026-02-27 20:15:50.722] [puff::index::jointLog] [info] rankSize = 19,592 2: [2026-02-27 20:15:50.722] [puff::index::jointLog] [info] edgeVecSize = 0 2: [2026-02-27 20:15:50.722] [puff::index::jointLog] [info] 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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 [Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec 2: [2026-02-27 20:15:50.739] [puff::index::jointLog] [info] mphf size = 0.0125198 MB 2: [2026-02-27 20:15:50.739] [puff::index::jointLog] [info] chunk size = 9,796 2: [2026-02-27 20:15:50.739] [puff::index::jointLog] [info] chunk 0 = [0, 9,796) 2: [2026-02-27 20:15:50.739] [puff::index::jointLog] [info] chunk 1 = [9,796, 19,562) 2: [2026-02-27 20:15:50.742] [puff::index::jointLog] [info] finished populating pos vector 2: [2026-02-27 20:15:50.742] [puff::index::jointLog] [info] writing index components 2: [2026-02-27 20:15:50.742] [puff::index::jointLog] [info] finished writing dense pufferfish index 2: [2026-02-27 20:15:50.742] [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: [2026-02-27 20:15:50.791] [jointLog] [info] setting maxHashResizeThreads to 12 2: ----------------------------------------- 2: | Loading contig table | Time = 31.12 us 2: ----------------------------------------- 2: size = 24 2: [2026-02-27 20:15:50.791] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. 2: [2026-02-27 20:15:50.791] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 2: [2026-02-27 20:15:50.791] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35. 2: [2026-02-27 20:15:50.791] [jointLog] [info] parsing read library format 2: [2026-02-27 20:15:50.791] [jointLog] [info] There is 1 library. 2: [2026-02-27 20:15:50.792] [jointLog] [info] Loading pufferfish index 2: [2026-02-27 20:15:50.792] [jointLog] [info] Loading dense pufferfish index. 2: ----------------------------------------- 2: | Loading contig offsets | Time = 440.2 us 2: ----------------------------------------- 2: ----------------------------------------- 2: | Loading reference lengths | Time = 5.96 us 2: ----------------------------------------- 2: ----------------------------------------- 2: | Loading mphf table | Time = 70.52 us 2: ----------------------------------------- 2: size = 19592 2: Number of ones: 23 2: Number of ones per inventory item: 512 2: Inventory entries filled: 1 2: ----------------------------------------- 2: | Loading contig boundaries | Time = 122.56 us 2: ----------------------------------------- 2: size = 19592 2: ----------------------------------------- 2: | Loading sequence | Time = 49.88 us 2: ----------------------------------------- 2: size = 18902 2: ----------------------------------------- 2: | Loading positions | Time = 90.4 us 2: ----------------------------------------- 2: size = 28562 2: ----------------------------------------- 2: | Loading reference sequence | Time = 43.76 us 2: ----------------------------------------- 2: ----------------------------------------- 2: | Loading reference accumulative lengths | Time = 5.56 us 2: ----------------------------------------- 2: [2026-02-27 20:15:50.793] [jointLog] [info] done 2: [2026-02-27 20:15:50.830] [jointLog] [info] Index contained 15 targets 2: [2026-02-27 20:15:50.830] [jointLog] [info] Number of decoys : 0 2: 2: 2: 2: 2: 2: 2: 2: 2: 2: 2: 2: 2: [2026-02-27 20:15:50.985] [jointLog] [info] Computed 28 rich equivalence classes for further processing 2: [2026-02-27 20:15:50.985] [jointLog] [info] Counted 10,000 total reads in the equivalence classes 2: [2026-02-27 20:15:50.990] [jointLog] [info] Number of mappings discarded because of alignment score : 67 2: [2026-02-27 20:15:50.990] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0 2: [2026-02-27 20:15:50.990] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 2: [2026-02-27 20:15:50.990] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0 2: [2026-02-27 20:15:50.990] [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: [2026-02-27 20:15:50.990] [jointLog] [info] Mapping rate = 100% 2: 2: [2026-02-27 20:15:50.990] [jointLog] [info] finished quantifyLibrary() 2: [2026-02-27 20:15:50.990] [jointLog] [info] Starting optimizer 2: [2026-02-27 20:15:50.992] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate 2: [2026-02-27 20:15:50.992] [jointLog] [info] iteration = 0 | max rel diff. = 14.87 2: [2026-02-27 20:15:50.997] [jointLog] [info] iteration = 100 | max rel diff. = 3.40868e-05 2: [2026-02-27 20:15:50.997] [jointLog] [info] Finished optimizer 2: [2026-02-27 20:15:50.997] [jointLog] [info] writing output 2: 2: Salmon (read) ran successfully 2/2 Test #2: salmon_read_test_quasi ........... Passed 1.12 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 1.39 sec make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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-aarch64-linux-gnu && make -j12 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-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/salmon-1.10.2+ds1 -B/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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-aarch64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-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-aarch64-linux-gnu' rm -Rvf /build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libsalmon_core.a' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake' removed directory '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/twopaco' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/libtwopaco.a' removed '/build/reproducible-path/salmon-1.10.2+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets-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/libgraphdump.a' 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/libntcard.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/menu.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/themetoggle.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/copybutton.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: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'salmon' in '../salmon_1.10.2+ds1-1_arm64.deb'. dpkg-deb: building package 'salmon-dbgsym' in '../salmon-dbgsym_1.10.2+ds1-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../salmon_1.10.2+ds1-1_arm64.buildinfo dpkg-genchanges --build=binary -O../salmon_1.10.2+ds1-1_arm64.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/3136144 and its subdirectories I: Current time: Fri Feb 27 20:16:25 -12 2026 I: pbuilder-time-stamp: 1772266585 Sun Jan 26 01:53:29 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Sun Jan 26 01:53:29 UTC 2025 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Sun Jan 26 02:07:24 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Sun Jan 26 02:07:25 UTC 2025 I: salmon_1.10.2+ds1-1_arm64.changes: Format: 1.8 Date: Wed, 16 Aug 2023 13:09:23 +0200 Source: salmon Binary: salmon salmon-dbgsym Architecture: arm64 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: b40feb841d7ca1a8104ce7c72a15f72909634533 41439448 salmon-dbgsym_1.10.2+ds1-1_arm64.deb 9009c856446f874b7a95997a0002756a9f718568 11618 salmon_1.10.2+ds1-1_arm64.buildinfo 74a240c99f0b379403670c17e383fa887ed84d5c 3162360 salmon_1.10.2+ds1-1_arm64.deb Checksums-Sha256: 880d3644ed6d3e1a21f4a64907114b5eef0978d4934722e3b09b07e014ce6aae 41439448 salmon-dbgsym_1.10.2+ds1-1_arm64.deb 921a9c997bcc7833153a5e414a73df548207088e0320be356cfd634bd3c4cd97 11618 salmon_1.10.2+ds1-1_arm64.buildinfo 165c0942700d91d3d05d8329ee187ac7aef98a29eee31b03d8581d210c9cc948 3162360 salmon_1.10.2+ds1-1_arm64.deb Files: 26b9aab1ec99cd883dfe54cee3e58b4c 41439448 debug optional salmon-dbgsym_1.10.2+ds1-1_arm64.deb 5715d3785f828af7d4cdd09b62c66b10 11618 science optional salmon_1.10.2+ds1-1_arm64.buildinfo 9ef05809c168b10a1bcee984224df300 3162360 science optional salmon_1.10.2+ds1-1_arm64.deb Sun Jan 26 02:07:26 UTC 2025 I: diffoscope 286 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_1-57399.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.bMU0zDvN/salmon_1.10.2+ds1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.bMU0zDvN/salmon_1.10.2+ds1-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.bMU0zDvN/salmon_1.10.2+ds1-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.bMU0zDvN/b1/salmon_1.10.2+ds1-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.bMU0zDvN/b2/salmon_1.10.2+ds1-1_arm64.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: 0.650s) 0.418s 6 calls xz 0.090s 6 calls diff 0.070s 2 calls cmp 0.070s 2 calls cmp (external) 0.001s 16 calls cmp (internal) ## compare_files (cumulative) (total time: 2.574s) 0.834s 1 call abc.DotChangesFile 0.731s 1 call abc.DebFile 0.690s 2 calls abc.XzFile 0.218s 1 call abc.DebDataTarFile 0.069s 1 call abc.TextFile 0.027s 1 call abc.TarFile 0.006s 1 call abc.Md5sumsFile ## container_extract (total time: 0.492s) 0.418s 6 calls diffoscope.comparators.xz.XzContainer 0.058s 98 calls diffoscope.comparators.deb.DebTarContainer 0.013s 8 calls diffoscope.comparators.deb.DebContainer 0.002s 6 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.325s) 0.325s 46 calls linediff ## has_same_content_as (total time: 0.073s) 0.055s 2 calls abc.DebFile 0.016s 1 call abc.DebDataTarFile 0.000s 4 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 2 calls abc.XzFile 0.000s 3 calls abc.TextFile 0.000s 2 calls abc.Md5sumsFile 0.000s 1 call diffoscope.comparators.binary.FilesystemFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call abc.TarFile ## main (total time: 100.350s) 100.349s 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: 98.812s) 98.809s 1 call html 0.002s 1 call text 0.001s 1 call json ## recognizes (total time: 0.499s) 0.391s 12 calls diffoscope.comparators.binary.FilesystemFile 0.052s 546 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.036s 108 calls diffoscope.comparators.debian.DebControlMember 0.020s 260 calls diffoscope.comparators.utils.archive.ArchiveMember ## specialize (total time: 0.797s) 0.797s 16 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 1min 40.652s CPU time consumed: 1min 40.622s Sun Jan 26 02:09:07 UTC 2025 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Sun Jan 26 02:09:07 UTC 2025 E: salmon failed to build reproducibly in trixie on arm64. Sun Jan 26 02:09:09 UTC 2025 I: Submitting .buildinfo files to external archives: Sun Jan 26 02:09:09 UTC 2025 I: Submitting 16K b1/salmon_1.10.2+ds1-1_arm64.buildinfo.asc Sun Jan 26 02:09:13 UTC 2025 I: Submitting 16K b2/salmon_1.10.2+ds1-1_arm64.buildinfo.asc Sun Jan 26 02:09:16 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jan 26 02:09:16 UTC 2025 I: Done submitting .buildinfo files. Sun Jan 26 02:09:16 UTC 2025 I: Removing signed salmon_1.10.2+ds1-1_arm64.buildinfo.asc files: removed './b1/salmon_1.10.2+ds1-1_arm64.buildinfo.asc' removed './b2/salmon_1.10.2+ds1-1_arm64.buildinfo.asc'