I: pbuilder: network access will be disabled during build I: Current time: Sat Jan 13 04:20:06 -12 2024 I: pbuilder-time-stamp: 1705162806 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_1.10.1+ds1-1.dsc] I: copying [./salmon_1.10.1+ds1.orig.tar.xz] I: copying [./salmon_1.10.1+ds1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Mar 13 08:29:02 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./salmon_1.10.1+ds1-1.dsc: no acceptable signature found dpkg-source: info: extracting salmon in salmon-1.10.1+ds1 dpkg-source: info: unpacking salmon_1.10.1+ds1.orig.tar.xz dpkg-source: info: unpacking salmon_1.10.1+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/2339344/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ee15c3cec5624c39b7687d55c8154717' 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='2339344' 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.qHQKbDOY/pbuilderrc_fYO6 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qHQKbDOY/b1 --logfile b1/build.log salmon_1.10.1+ds1-1.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 2023 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 23 2023 more -rwsr-xr-x 1 root root 59704 Mar 23 2023 mount -rwxr-xr-x 1 root root 18744 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar -rwxr-xr-x 1 root root 14520 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 23 2023 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/2339344/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev, libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev (>> 2.0), libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, python3-docs-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev, libsimde-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18148 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} catch2{a} cmake{a} cmake-data{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} libarchive-zip-perl{a} libarchive13{a} libboost-atomic1.74-dev{a} libboost-atomic1.74.0{a} libboost-chrono1.74-dev{a} libboost-chrono1.74.0{a} libboost-date-time1.74-dev{a} libboost-date-time1.74.0{a} libboost-filesystem-dev{a} libboost-filesystem1.74-dev{a} libboost-filesystem1.74.0{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost-thread-dev{a} libboost-thread1.74-dev{a} libboost-thread1.74.0{a} libboost-timer-dev{a} libboost-timer1.74-dev{a} libboost-timer1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libbwa-dev{a} libbz2-dev{a} libcereal-dev{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdivsufsort-dev{a} libdivsufsort3{a} libeigen3-dev{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfmt-dev{a} libfmt9{a} libgff-dev{a} libhtscodecs-dev{a} libhtscodecs2{a} libhwloc15{a} libicu-dev{a} libicu72{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} libjsoncpp25{a} libldap-2.5-0{a} liblocale-gettext-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5{a} libpthread-stubs0-dev{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsimde-dev{a} libsparsehash-dev{a} libspdlog-dev{a} libspdlog1.10{a} libssh2-1{a} libstaden-read-dev{a} libstaden-read14{a} libsub-override-perl{a} libtbb-dev{a} libtbb12{a} libtbbbind-2-5{a} libtbbmalloc2{a} libtclap-dev{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} media-types{a} openssl{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python-babel-localedata{a} python-requests-doc{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-distutils{a} python3-doc{a} python3-docs-theme{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-requests{a} python3-roman{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-tz{a} python3-urllib3{a} python3.11{a} python3.11-doc{a} python3.11-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 libarchive-cpio-perl libhwloc-plugins libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx psmisc publicsuffix python3-pil wget 0 packages upgraded, 175 newly installed, 0 to remove and 0 not upgraded. Need to get 119 MB of archives. After unpacking 657 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 fonts-lato all 2.0-2.1 [2696 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 13 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2023c-5+deb12u1 [296 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.11-1~deb12u2 [1419 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 catch2 amd64 2.13.10-1 [458 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libarchive13 amd64 3.6.2-1 [343 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u4 [390 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 librhash0 amd64 1.4.3-3 [134 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 cmake-data all 3.25.1-1 [2026 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 cmake amd64 3.25.1-1 [8692 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 docutils-common all 0.19+dfsg-6 [127 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 docutils-doc all 0.19+dfsg-6 [1098 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 help2man amd64 1.49.3 [198 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 icu-devtools amd64 72.1-3 [206 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libboost-atomic1.74.0 amd64 1.74.0+ds1-21 [220 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libboost-atomic1.74-dev amd64 1.74.0+ds1-21 [221 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libboost-chrono1.74.0 amd64 1.74.0+ds1-21 [228 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libboost-chrono1.74-dev amd64 1.74.0+ds1-21 [235 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libboost-date-time1.74.0 amd64 1.74.0+ds1-21 [217 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libboost-serialization1.74.0 amd64 1.74.0+ds1-21 [317 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libboost-serialization1.74-dev amd64 1.74.0+ds1-21 [359 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libboost-date-time1.74-dev amd64 1.74.0+ds1-21 [226 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem1.74.0 amd64 1.74.0+ds1-21 [258 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libboost-system1.74.0 amd64 1.74.0+ds1-21 [218 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libboost-system1.74-dev amd64 1.74.0+ds1-21 [219 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem1.74-dev amd64 1.74.0+ds1-21 [279 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem-dev amd64 1.74.0.3 [4368 B] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74.0 amd64 1.74.0+ds1-21 [487 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libicu-dev amd64 72.1-3 [10.3 MB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74-dev amd64 1.74.0+ds1-21 [557 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams1.74-dev amd64 1.74.0+ds1-21 [248 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams-dev amd64 1.74.0.3 [4316 B] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74.0 amd64 1.74.0+ds1-21 [329 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options1.74-dev amd64 1.74.0+ds1-21 [357 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libboost-program-options-dev amd64 1.74.0.3 [4340 B] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libboost-system-dev amd64 1.74.0.3 [4468 B] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libboost-thread1.74.0 amd64 1.74.0+ds1-21 [257 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 libboost-thread1.74-dev amd64 1.74.0+ds1-21 [267 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libboost-thread-dev amd64 1.74.0.3 [4356 B] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libboost-timer1.74.0 amd64 1.74.0+ds1-21 [226 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libboost-timer1.74-dev amd64 1.74.0+ds1-21 [229 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libboost-timer-dev amd64 1.74.0.3 [4456 B] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libbwa-dev amd64 0.7.17-7+b2 [156 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libbz2-dev amd64 1.0.8-5+b1 [30.9 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 rapidjson-dev all 1.1.0+dfsg2-7.1 [97.7 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libcereal-dev amd64 1.3.2+dfsg-4 [221 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u4 [385 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libcurl4-gnutls-dev amd64 7.88.1-10+deb12u4 [485 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 libdivsufsort-dev amd64 2.0.1-5 [19.1 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 libfmt9 amd64 9.1.0+ds1-2 [113 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 libfmt-dev amd64 9.1.0+ds1-2 [171 kB] Get: 117 http://deb.debian.org/debian bookworm/main amd64 libgff-dev amd64 2.0.0-3 [154 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs-dev amd64 1.3.0-4 [2866 kB] Get: 120 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 libjellyfish-2.0-2 amd64 2.3.0-15+b3 [63.2 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 libjellyfish-2.0-dev amd64 2.3.0-15+b3 [136 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 libjemalloc2 amd64 5.3.0-1 [275 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 libjemalloc-dev amd64 5.3.0-1 [494 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get: 132 http://deb.debian.org/debian bookworm/main amd64 libsimde-dev all 0.7.4~rc2-2 [377 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 libspdlog1.10 amd64 1:1.10.0+ds-0.4 [130 kB] Get: 135 http://deb.debian.org/debian bookworm/main amd64 libspdlog-dev amd64 1:1.10.0+ds-0.4 [209 kB] Get: 136 http://deb.debian.org/debian bookworm/main amd64 libstaden-read14 amd64 1.14.15-1 [265 kB] Get: 137 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 138 http://deb.debian.org/debian bookworm/main amd64 libstaden-read-dev amd64 1.14.15-1 [344 kB] Get: 139 http://deb.debian.org/debian bookworm/main amd64 libtbbmalloc2 amd64 2021.8.0-2 [46.3 kB] Get: 140 http://deb.debian.org/debian bookworm/main amd64 libtbbbind-2-5 amd64 2021.8.0-2 [13.5 kB] Get: 141 http://deb.debian.org/debian bookworm/main amd64 libtbb12 amd64 2021.8.0-2 [79.1 kB] Get: 142 http://deb.debian.org/debian bookworm/main amd64 libtbb-dev amd64 2021.8.0-2 [192 kB] Get: 143 http://deb.debian.org/debian bookworm/main amd64 libtclap-dev amd64 1.2.5-1+b1 [3360 kB] Get: 144 http://deb.debian.org/debian bookworm/main amd64 python-babel-localedata all 2.10.3-1 [5615 kB] Get: 145 http://deb.debian.org/debian bookworm/main amd64 python-requests-doc all 2.28.1+dfsg-1 [183 kB] Get: 146 http://deb.debian.org/debian bookworm/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 147 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 148 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get: 149 http://deb.debian.org/debian bookworm/main amd64 python3-babel all 2.10.3-1 [103 kB] Get: 150 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get: 151 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 152 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 153 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 154 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get: 155 http://deb.debian.org/debian bookworm/main amd64 python3.11-doc all 3.11.2-6 [12.6 MB] Get: 156 http://deb.debian.org/debian bookworm/main amd64 python3-doc all 3.11.2-1 [9208 B] Get: 157 http://deb.debian.org/debian bookworm/main amd64 python3-docs-theme all 2022.1-1 [14.4 kB] Get: 158 http://deb.debian.org/debian bookworm/main amd64 python3-roman all 3.3-3 [9880 B] Get: 159 http://deb.debian.org/debian bookworm/main amd64 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 160 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1 [39.4 kB] Get: 161 http://deb.debian.org/debian bookworm/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 162 http://deb.debian.org/debian bookworm/main amd64 python3-markupsafe amd64 2.1.2-1+b1 [13.2 kB] Get: 163 http://deb.debian.org/debian bookworm/main amd64 python3-jinja2 all 3.1.2-1 [119 kB] Get: 164 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 165 http://deb.debian.org/debian bookworm/main amd64 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 166 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get: 167 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1 [117 kB] Get: 168 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 169 http://deb.debian.org/debian bookworm/main amd64 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 170 http://deb.debian.org/debian bookworm/main amd64 sphinx-common all 5.3.0-4 [653 kB] Get: 171 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx all 5.3.0-4 [549 kB] Get: 172 http://deb.debian.org/debian bookworm/main amd64 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB] Get: 173 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx-rtd-theme all 1.2.0+dfsg-1 [27.7 kB] Get: 174 http://deb.debian.org/debian bookworm/main amd64 rapmap-dev all 0.15.0+dfsg-3 [193 kB] Get: 175 http://deb.debian.org/debian bookworm/main amd64 sphinx-doc all 5.3.0-4 [2307 kB] Fetched 119 MB in 38s (3159 kB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 18148 files and directories currently installed.) Preparing to unpack .../fonts-lato_2.0-2.1_all.deb ... Unpacking fonts-lato (2.0-2.1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-5_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (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 ... 18504 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../3-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 18938 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package tzdata. Preparing to unpack .../002-tzdata_2023c-5+deb12u1_all.deb ... Unpacking tzdata (2023c-5+deb12u1) ... 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Setting up libboost-iostreams-dev:amd64 (1.74.0.3) ... Setting up python3-markupsafe (2.1.2-1+b1) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... Setting up python3-roman (3.3-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up python3-packaging (23.0-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up python3-idna (3.3-1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up python3-babel (2.10.3-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-docs-theme (2022.1-1) ... Setting up python3-pygments (2.14.0+dfsg-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up python3-requests (2.28.1+dfsg-1) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.19+dfsg-6) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.19+dfsg-6) ... Setting up python3-sphinx (5.3.0-4) ... Setting up python3-sphinx-rtd-theme (1.2.0+dfsg-1) ... Processing triggers for ca-certificates (20230311) ... 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-1.10.1+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_1.10.1+ds1-1_source.changes dpkg-buildpackage: info: source package salmon dpkg-buildpackage: info: source version 1.10.1+ds1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with sphinxdoc debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/doc' rm -rf build/* make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/doc' rm -rf tests/unitTests make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+ds1/external/install/src/rapmap cp -av /usr/share/rapmap/src/* /build/reproducible-path/salmon-1.10.1+ds1/external/install/src/rapmap '/usr/share/rapmap/src/HitManager.cpp' -> '/build/reproducible-path/salmon-1.10.1+ds1/external/install/src/rapmap/HitManager.cpp' '/usr/share/rapmap/src/RapMapFileSystem.cpp' -> '/build/reproducible-path/salmon-1.10.1+ds1/external/install/src/rapmap/RapMapFileSystem.cpp' '/usr/share/rapmap/src/RapMapSAIndex.cpp' -> '/build/reproducible-path/salmon-1.10.1+ds1/external/install/src/rapmap/RapMapSAIndex.cpp' '/usr/share/rapmap/src/RapMapSAIndexer.cpp' -> '/build/reproducible-path/salmon-1.10.1+ds1/external/install/src/rapmap/RapMapSAIndexer.cpp' '/usr/share/rapmap/src/RapMapUtils.cpp' -> '/build/reproducible-path/salmon-1.10.1+ds1/external/install/src/rapmap/RapMapUtils.cpp' '/usr/share/rapmap/src/bit_array.c' -> '/build/reproducible-path/salmon-1.10.1+ds1/external/install/src/rapmap/bit_array.c' '/usr/share/rapmap/src/rank9b.cpp' -> '/build/reproducible-path/salmon-1.10.1+ds1/external/install/src/rapmap/rank9b.cpp' dh_auto_configure -- -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE -DCMAKE_BUILD_TYPE=Release -DUSE_SHARED_LIBS=TRUE .. CC: gcc CC version: -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Detected non-ARM host. Setting USE_ARM to false. version: 1.10.1 -- 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 running cd "/build/reproducible-path/salmon-1.10.1+ds1" && cp -r ./debian/external ./ 2>&1 -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.13") -- 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 "5.4.1") 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 =========================================== -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.59.0") found components: iostreams system filesystem timer chrono program_options BOOST_INCLUDEDIR = BOOST_LIBRARYDIR = Boost_FOUND = TRUE BOOST ROOT = BOOST INCLUDE DIR = /usr/include BOOST INCLUDE DIRS = /usr/include BOOST LIB DIR = /usr/lib/x86_64-linux-gnu BOOST LIBRARIES = Boost::iostreams;Boost::system;Boost::filesystem;Boost::timer;Boost::chrono;Boost::program_options -- Found cereal: /usr/include (found suitable version "1.3.2", minimum required is "1.3.2") -- cereal found (include: /usr/include) FOUND SUITABLE TBB VERSION : 2021.8.0 -- libgff ver. 2.0.0 found. -- include: /usr/include/ -- lib : /usr/lib/ -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "7.88.1") -- Found libstadenio: /usr/lib/x86_64-linux-gnu/libstaden-read.so (Required is at least version "1.14.15") -- Staden IOLib found (include: /usr/include) -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Found Jemalloc: /usr/lib/x86_64-linux-gnu/libjemalloc.so (found version "5.3.0-0-g54eaed1d8b56b1aa528be3bdd1877e59c56fa90c") Found Jemalloc library --- using this memory allocator CPACK_SOURCE_IGNORE_FILES = /src/PCA.cpp;/src/PCAUtils.cpp;/build/;/scripts/AggregateToGeneLevel.py;/scripts/ExpressionTools.py;/scripts/GenerateExpressionFiles.sh;/scripts/ParseSoftFile.py;/scripts/PlotCorrelation.py;/scripts/junk;/scripts/sfstrace.log;/scripts/SFPipeline.py;/bin/;/lib/;/sample_data/;PublishREADMEToWebsite.sh;/external/;/src/obsolete/;/include/obsolete/;WebsiteHeader.txt;/experimental_configs/;.git/ CC: /usr/bin/cc CC version: version: 1.0.0 Building basic pufferfish components for salmon setting -DHAVE_NUMERIC_LIMITS128 -- setting COMPACT_VECTOR_DIR for graphdump to be /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump 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-1.10.1+ds1/src/LibraryFormat.cpp adding /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump to include path for libpuffer fetched path for compact_vector as [/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump] NO_IPO = FALSE TBB_LIBRARIES = TBB_LIB_INSTALL_DIR = TBBGLOBS = -- Configuring done -- Generating done 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-1.10.1+ds1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1' dh_auto_build cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/salmon-1.10.1+ds1 -B/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend make -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend make -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.1+ds1 /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/ntcard /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/DependInfo.cmake --color= make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.1+ds1 /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/DependInfo.cmake --color= make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.1+ds1 /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.1+ds1 /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.1+ds1 /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.1+ds1 /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.1+ds1 /build/reproducible-path/salmon-1.10.1+ds1/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake --color= make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend make -f src/CMakeFiles/UnitTestsMain.dir/build.make src/CMakeFiles/UnitTestsMain.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.1+ds1 /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.1+ds1 /build/reproducible-path/salmon-1.10.1+ds1/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.1+ds1 /build/reproducible-path/salmon-1.10.1+ds1/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/UnitTestsMain.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build make -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' make[4]: Entering 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src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -MD -MT src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -MF CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o.d -o CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -c /build/reproducible-path/salmon-1.10.1+ds1/src/jellyfish/mer_dna.cc [ 13%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/ksw2pp/ksw2_extz.c [ 14%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -mno-sse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c [ 15%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/ksw2pp/ksw2_gg.c [ 16%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -MF CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o.d -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp [ 17%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2.c [ 18%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -std=c++14 -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-1.10.1+ds1/external/pufferfish/external/ntcard/Common/Fcontrol.cpp [ 19%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c [ 20%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -msse -msse2 -msse3 -mssse3 -msse4 -msse4.1 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c [ 21%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o [ 21%] Building CXX object src/CMakeFiles/salmon_core.dir/backtrace.cc.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -std=c++14 -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-1.10.1+ds1/external/pufferfish/external/ntcard/nthll.cpp cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/backtrace.cc [ 21%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2_sse.c [ 22%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp [ 23%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/SingleCellProtocols.cpp [ 24%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp [ 25%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/xxhash.c.o -MF CMakeFiles/salmon_core.dir/xxhash.c.o.d -o CMakeFiles/salmon_core.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.10.1+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 make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' [ 25%] Built target ksw2pp_sse2 [ 26%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/TranscriptGroup.cpp [ 27%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/EffectiveLengthStats.cpp [ 28%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/LibraryFormat.cpp [ 29%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/AlevinUtils.cpp [ 30%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/GenomicFeature.cpp make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' [ 30%] Built target ksw2pp_sse4 [ 31%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/VersionChecker.cpp [ 32%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/SBModel.cpp [ 33%] Linking CXX static library libntcard.a cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -E cmake_link_script CMakeFiles/ntcard.dir/link.txt --verbose=1 /usr/bin/ar qc libntcard.a CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o CMakeFiles/ntcard.dir/nthll.cpp.o /usr/bin/ranlib libntcard.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' [ 33%] Built target ntcard [ 34%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o -MF CMakeFiles/twopaco.dir/compressedstring.cpp.o.d -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp [ 35%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o [ 36%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o -MF CMakeFiles/twopaco.dir/test.cpp.o.d -o CMakeFiles/twopaco.dir/test.cpp.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' [ 36%] 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-1.10.1+ds1/obj-x86_64-linux-gnu' cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.1+ds1 /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' [ 37%] Linking CXX static library libksw2pp.a cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake [ 37%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -MF CMakeFiles/twopaco.dir/vertexenumerator.cpp.o.d -o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-12" cr 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-12" libksw2pp.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' [ 37%] Built target ksw2pp [ 38%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/PufferfishIndex.cpp [ 38%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/FastxParser.cpp [ 39%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -MF CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp [ 40%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o -MF CMakeFiles/twopaco.dir/common.cpp.o.d -o CMakeFiles/twopaco.dir/common.cpp.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphconstructor/common.cpp [ 41%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/StadenUtils.cpp [ 42%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/SalmonUtils.cpp In file included from /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, from /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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 > > > >]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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 > >]' /build/reproducible-path/salmon-1.10.1+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 >]' /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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> > >]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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>]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+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); | ^~~~~~~~ [ 43%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp [ 43%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/PufferfishLossyIndex.cpp [ 44%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/DistributionUtils.cpp [ 45%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/SalmonExceptions.cpp [ 46%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/SalmonStringUtils.cpp [ 47%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/SimplePosBias.cpp /build/reproducible-path/salmon-1.10.1+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-1.10.1+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 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 48%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/SGSmooth.cpp [ 48%] Building CXX object src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/external/install/src/pufferfish/metro/metrohash64.cpp [ 49%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/edlib.cpp [ 50%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/Util.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/Util.cpp [ 51%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9sel.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/rank9sel.cpp [ 52%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/rank9b.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/rank9b.cpp [ 53%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishValidate.cpp.o cd 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-c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/PufferfishValidate.cpp [ 54%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishStats.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/PufferfishStats.cpp [ 55%] Linking CXX static library libgraphdump.a cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -P CMakeFiles/graphdump.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphdump.dir/link.txt --verbose=1 /usr/bin/ar qc libgraphdump.a CMakeFiles/graphdump.dir/graphdump.cpp.o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o /usr/bin/ranlib libgraphdump.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' [ 55%] Built target graphdump [ 55%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/PufferfishExamine.cpp [ 56%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/PufferfishTestLookup.cpp [ 57%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/PufferfishKmerQuery.cpp /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/PufferfishTestLookup.cpp: In function 'std::vector get_kmers(const std::string&, uint32_t)': /build/reproducible-path/salmon-1.10.1+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) { | ~~~~~~~~~^ [ 58%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/FastxParser.cpp [ 59%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp [ 60%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/PufferFS.cpp [ 61%] Building C object external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cc -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o -MF CMakeFiles/puffer.dir/xxhash.c.o.d -o CMakeFiles/puffer.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/xxhash.c cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C [ 62%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp [ 63%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/MemCollector.cpp In file included from /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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 > > > >]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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 > >]' /build/reproducible-path/salmon-1.10.1+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 >]' /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:161:25: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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> > >]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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>]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:414:43: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+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); | ^~~~~~~~ [ 63%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/MemChainer.cpp [ 64%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/PuffAligner.cpp [ 65%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/PufferfishAligner.cpp [ 66%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/RefSeqConstructor.cpp [ 67%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/external/pufferfish/src/metro/metrohash64.cpp [ 68%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.1+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -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-1.10.1+ds1/src/LibraryFormat.cpp [ 69%] Linking CXX static library libalevin_core.a cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-12" cr libalevin_core.a CMakeFiles/alevin_core.dir/edlib.cpp.o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o In file included from /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:4: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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 > > > >]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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 > >]' /build/reproducible-path/salmon-1.10.1+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 >]' /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:264:46: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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 > >]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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>]' /build/reproducible-path/salmon-1.10.1+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>]' /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:490:26: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+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); | ^~~~~~~~ "/usr/bin/gcc-ranlib-12" libalevin_core.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' [ 69%] Built target alevin_core In file included from /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include/RefSeqConstructor.hpp:5, from /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/RefSeqConstructor.cpp:1: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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 > >]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/RefSeqConstructor.cpp:466:16: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+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); | ^~~~~~~~ [ 70%] Linking CXX static library libsalmon_core.a cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1 "/usr/bin/gcc-ar-12" cr 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-12" libsalmon_core.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' [ 70%] Built target salmon_core [ 71%] Linking CXX static library libUnitTestsMain.a cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/UnitTestsMain.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-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-1.10.1+ds1/obj-x86_64-linux-gnu' [ 71%] Built target UnitTestsMain make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/depend make[4]: Entering directory 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/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_TIMER_DYN_LINK -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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 -std=c++14 -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-1.10.1+ds1/tests/GCSampleTests.cpp [ 74%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_TIMER_DYN_LINK -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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 -std=c++14 -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-1.10.1+ds1/src/FragmentLengthDistribution.cpp cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_TIMER_DYN_LINK -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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 -std=c++14 -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-1.10.1+ds1/external/install/src/pufferfish/rank9b.cpp [ 75%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_TIMER_DYN_LINK -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -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 -std=c++14 -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-1.10.1+ds1/tests/LibraryTypeTests.cpp In file included from /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include/digestpp/algorithm/sha2.hpp:9, from /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include/digestpp/digestpp.hpp:6, from /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:537:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/digestpp.hpp:5: /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp:170:19, inlined from 'bool extractFasta(std::string&, std::string&, uint32_t&)' at /build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:536:26: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/external/pufferfish/include/digestpp/hasher.hpp: In function 'bool extractFasta(std::string&, std::string&, uint32_t&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/external/pufferfish/src/FixFasta.cpp:188:24: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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-1.10.1+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-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitTests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now 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-1.10.1+ds1/lib -L/build/reproducible-path/salmon-1.10.1+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex libsalmon_core.a libalevin_core.a -lgff libUnitTestsMain.a /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_timer.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/x86_64-linux-gnu/libstaden-read.so /usr/lib/x86_64-linux-gnu/libhtscodecs.so /usr/lib/x86_64-linux-gnu/libcurl.so -lz -lm -llzma -lbz2 -ltbb -ltbbmalloc -lgomp -lrt -ldl Copying unitTests cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E copy /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src/unitTests /build/reproducible-path/salmon-1.10.1+ds1/tests/unitTests make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' [ 76%] Built target unitTests [ 77%] Linking CXX static library libpuffer.a cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/puffer.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/puffer.dir/link.txt --verbose=1 /usr/bin/ar qc libpuffer.a CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o CMakeFiles/puffer.dir/edlib.cpp.o CMakeFiles/puffer.dir/Util.cpp.o CMakeFiles/puffer.dir/rank9sel.cpp.o CMakeFiles/puffer.dir/rank9b.cpp.o CMakeFiles/puffer.dir/PufferfishValidate.cpp.o CMakeFiles/puffer.dir/PufferfishStats.cpp.o CMakeFiles/puffer.dir/PufferfishTestLookup.cpp.o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o CMakeFiles/puffer.dir/FastxParser.cpp.o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o CMakeFiles/puffer.dir/PufferFS.cpp.o CMakeFiles/puffer.dir/xxhash.c.o CMakeFiles/puffer.dir/FixFasta.cpp.o CMakeFiles/puffer.dir/MemCollector.cpp.o CMakeFiles/puffer.dir/MemChainer.cpp.o CMakeFiles/puffer.dir/PuffAligner.cpp.o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o /usr/bin/ranlib libpuffer.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' [ 77%] Built target puffer [ 78%] Linking CXX static library libtwopaco.a cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -P CMakeFiles/twopaco.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/cmake -E cmake_link_script CMakeFiles/twopaco.dir/link.txt --verbose=1 /usr/bin/ar qc libtwopaco.a CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o CMakeFiles/twopaco.dir/constructor.cpp.o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o CMakeFiles/twopaco.dir/compressedstring.cpp.o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o CMakeFiles/twopaco.dir/test.cpp.o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o CMakeFiles/twopaco.dir/common.cpp.o /usr/bin/ranlib libtwopaco.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' [ 78%] Built target 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-I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -MD -MT 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-I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/Salmon.cpp [ 83%] Building CXX 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-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 -std=c++14 -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-1.10.1+ds1/src/WhiteList.cpp cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/SalmonQuantify.cpp [ 90%] Building CXX object src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/FragmentLengthDistribution.cpp [ 91%] Building CXX object src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/FragmentStartPositionDistribution.cpp In file included from /build/reproducible-path/salmon-1.10.1+ds1/include/pcg_random.hpp:104, from /build/reproducible-path/salmon-1.10.1+ds1/src/CollapsedGibbsSampler.cpp:22: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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__); | ^~~~~~~~ [ 92%] Building CXX object src/CMakeFiles/salmon.dir/GZipWriter.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/GZipWriter.cpp [ 93%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/SalmonQuantMerge.cpp In file included from /build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/sparsepp/spp.h:65, from /build/reproducible-path/salmon-1.10.1+ds1/include/AlevinUtils.hpp:47, from /build/reproducible-path/salmon-1.10.1+ds1/include/Graph.hpp:8, from /build/reproducible-path/salmon-1.10.1+ds1/src/Graph.cpp:1: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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>]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Graph.cpp:10:29: required from here /build/reproducible-path/salmon-1.10.1+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++/12/bits/stl_algobase.h:64, from /usr/include/c++/12/string:50, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/streambuf:41, from /usr/include/c++/12/bits/streambuf_iterator.h:35, from /usr/include/c++/12/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-1.10.1+ds1/include/Graph.hpp:4: /usr/include/c++/12/bits/stl_pair.h:185:12: note: 'struct std::pair, unsigned int>' declared here 185 | struct pair | ^~~~ [ 94%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/ProgramOptionsGenerator.cpp In file included from /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:60: /build/reproducible-path/salmon-1.10.1+ds1/include/BarcodeModel.hpp: In function 'void alevin::model::coinTossBarcodeModel(std::string, const std::vector >&, MapT&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/include/BarcodeModel.hpp:168:31: note: use reference type to prevent copying 168 | for(const std::string trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & [ 94%] Building CXX object src/CMakeFiles/salmon.dir/FASTAParser.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/FASTAParser.cpp [ 95%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/AlignmentModel.cpp /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:1084:23: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:1094:25: required from here /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:1110:25: required from here /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:1122:23: required from here /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2777:62: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2777:62: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ [ 96%] Building CXX object src/CMakeFiles/salmon.dir/ONTAlignmentModel.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/ONTAlignmentModel.cpp /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2791:62: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2791:62: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2804:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2804:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2817:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2817:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2830:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2830:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2843:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2843:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2856:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2856:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2869:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2869:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2882:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2882:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2895:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2895:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2908:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2908:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2923:62: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2923:62: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2940:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2940:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2954:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:1129:23: required from here /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.1+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-1.10.1+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:5 = fastx_parser::FastxParser; auto:6 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/SalmonAlevin.cpp:2954:58: required from here /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 397 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:1136:23: required from here /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:1143:23: required from here /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:1150:23: required from here /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:1157:23: required from here /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:1164:23: required from here /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:1171:23: required from here /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:1177:23: required from here /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:1183:23: required from here /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:1189:23: required from here /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string' [-Wrange-loop-construct] /build/reproducible-path/salmon-1.10.1+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying 488 | for (const auto trueBarcode: trueBarcodes){ | ^~~~~~~~~~~ | & In file included from /build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/sparsepp/spp.h:65, from /build/reproducible-path/salmon-1.10.1+ds1/include/AlevinUtils.hpp:47, from /build/reproducible-path/salmon-1.10.1+ds1/include/Graph.hpp:8, from /build/reproducible-path/salmon-1.10.1+ds1/include/DedupUMI.hpp:4, from /build/reproducible-path/salmon-1.10.1+ds1/src/DedupUMI.cpp:1: /build/reproducible-path/salmon-1.10.1+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-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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>&]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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> >]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+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]' /build/reproducible-path/salmon-1.10.1+ds1/src/DedupUMI.cpp:39:25: required from here /build/reproducible-path/salmon-1.10.1+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++/12/bits/stl_algobase.h:64, from /usr/include/c++/12/string:50, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/streambuf:41, from /usr/include/c++/12/bits/streambuf_iterator.h:35, from /usr/include/c++/12/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-1.10.1+ds1/include/Graph.hpp:4: /usr/include/c++/12/bits/stl_pair.h:185:12: note: 'struct std::pair, unsigned int>' declared here 185 | struct pair | ^~~~ [ 97%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentCommon.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/AlignmentCommon.cpp [ 98%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantifyAlignments.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/SalmonQuantifyAlignments.cpp [ 99%] Building CXX object src/CMakeFiles/salmon.dir/BAMUtils.cpp.o cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.1+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.1+ds1/external -I/build/reproducible-path/salmon-1.10.1+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.1+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.1+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -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-1.10.1+ds1/src/BAMUtils.cpp /build/reproducible-path/salmon-1.10.1+ds1/src/ONTAlignmentModel.cpp: In constructor 'ONTAlignmentModel::ONTAlignmentModel(double, uint32_t)': /build/reproducible-path/salmon-1.10.1+ds1/src/ONTAlignmentModel.cpp:17:45: warning: unused parameter 'alpha' [-Wunused-parameter] 17 | ONTAlignmentModel::ONTAlignmentModel(double alpha, uint32_t readBins) | ~~~~~~~^~~~~ /build/reproducible-path/salmon-1.10.1+ds1/src/ONTAlignmentModel.cpp: In member function 'double ONTAlignmentModel::logLikelihood(const UnpairedRead&, const UnpairedRead&, Transcript&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/ONTAlignmentModel.cpp: In member function 'void ONTAlignmentModel::update(const UnpairedRead&, const UnpairedRead&, Transcript&, double, double)': /build/reproducible-path/salmon-1.10.1+ds1/src/ONTAlignmentModel.cpp:137:56: warning: unused parameter 'p' [-Wunused-parameter] 137 | Transcript& ref, double p, double mass) { | ~~~~~~~^ /build/reproducible-path/salmon-1.10.1+ds1/src/ONTAlignmentModel.cpp: In member function 'void ONTAlignmentModel::printModel(std::ostream&)': /build/reproducible-path/salmon-1.10.1+ds1/src/ONTAlignmentModel.cpp:194:50: warning: unused parameter 'os' [-Wunused-parameter] 194 | void ONTAlignmentModel::printModel(std::ostream& os) { | ~~~~~~~~~~~~~~^~ /build/reproducible-path/salmon-1.10.1+ds1/src/AlignmentModel.cpp: In member function 'AlignmentModel::AlnModelProb AlignmentModel::logLikelihood(bam_seq_t*, bam_seq_t*, Transcript&, std::vector >&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/AlignmentModel.cpp: In member function 'double AlignmentModel::logLikelihood(const ReadPair&, const ReadPair&, Transcript&)': /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/src/AlignmentModel.cpp: In member function 'void AlignmentModel::update(const ReadPair&, const ReadPair&, Transcript&, double, double)': /build/reproducible-path/salmon-1.10.1+ds1/src/AlignmentModel.cpp:429:66: warning: unused parameter 'primary' [-Wunused-parameter] 429 | void AlignmentModel::update(const ReadPair& hit, const ReadPair& primary, | ~~~~~~~~~~~~~~~~^~~~~~~ [100%] Linking CXX executable salmon cd /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.1+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now 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-1.10.1+ds1/lib -L/build/reproducible-path/salmon-1.10.1+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" ../external/pufferfish/src/libpuffer.a libsalmon_core.a ../external/pufferfish/external/twopaco/graphconstructor/libtwopaco.a ../external/pufferfish/external/twopaco/graphdump/libgraphdump.a ../external/pufferfish/external/ntcard/libntcard.a -lgff -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex /usr/lib/x86_64-linux-gnu/libcurl.so -lz -lm /usr/lib/x86_64-linux-gnu/libstaden-read.so /usr/lib/x86_64-linux-gnu/libhtscodecs.so -llzma -lbz2 -lgomp ../external/pufferfish/src/libksw2pp.a libalevin_core.a -ltbb -ltbbmalloc -ljemalloc -lrt -ldl make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' [100%] Built target salmon make[3]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' mv doc/source/license.rst doc/ # unused PYTHONPATH=. http_proxy='127.0.0.1:9' sphinx-build -N -bhtml doc/source doc/build/html Running Sphinx v5.3.0 making output directory... done WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0 po files that are out of date building [html]: targets for 6 source files that are out of date updating environment: [new config] 6 added, 0 changed, 0 removed reading sources... [ 16%] alevin reading sources... [ 33%] building reading sources... [ 50%] file_formats reading sources... [ 66%] index reading sources... [ 83%] library_type reading sources... [100%] salmon /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:36: WARNING: Title underline too short. Providing multiple read files to Alevin ------------ /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:36: WARNING: Title underline too short. Providing multiple read files to Alevin ------------ /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:56: WARNING: Explicit markup ends without a blank line; unexpected unindent. /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:79: WARNING: Block quote ends without a blank line; unexpected unindent. /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:83: WARNING: Title overline too short. """""""""""" ``--whitelist`` """""""""""" /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:83: WARNING: Title overline too short. """""""""""" ``--whitelist`` """""""""""" /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:93: WARNING: Title overline too short. """""""""""" ``--noQuant`` """""""""""" /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:93: WARNING: Title overline too short. """""""""""" ``--noQuant`` """""""""""" /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:99: WARNING: Title overline too short. """""""""""" ``--noDedup`` """""""""""" /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:99: WARNING: Title overline too short. """""""""""" ``--noDedup`` """""""""""" /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:127: WARNING: Title overline too short. """""""""""" ``--dumpBfh`` """""""""""" /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:127: WARNING: Title overline too short. """""""""""" ``--dumpBfh`` """""""""""" /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:133: WARNING: Title overline too short. """""""""""" ``--dumpFeatures`` """""""""""" /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:133: WARNING: Title overline too short. """""""""""" ``--dumpFeatures`` """""""""""" /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:139: WARNING: Title overline too short. """""""""""" ``--dumpMtx`` """""""""""" /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:139: WARNING: Title overline too short. """""""""""" ``--dumpMtx`` """""""""""" /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:155: WARNING: Title overline too short. """""""""""""""""""""" ``--numCellBootstraps`` """""""""""""""""""""" /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:155: WARNING: Title overline too short. """""""""""""""""""""" ``--numCellBootstraps`` """""""""""""""""""""" /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:214: WARNING: Title underline too short. Output Quality Check ------------- /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:214: WARNING: Title underline too short. Output Quality Check ------------- /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:263: WARNING: Title underline too short. BibTex ---- /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:263: WARNING: Title underline too short. BibTex ---- /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:297: WARNING: Duplicate explicit target name: "swish". /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:297: WARNING: Footnote [#] is not referenced. /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:299: WARNING: Footnote [#] is not referenced. /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:301: WARNING: Footnote [#] is not referenced. /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:303: WARNING: Footnote [#] is not referenced. /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:305: WARNING: Footnote [#] is not referenced. /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:307: WARNING: Footnote [#] is not referenced. /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:309: WARNING: Footnote [#] is not referenced. /build/reproducible-path/salmon-1.10.1+ds1/doc/source/alevin.rst:311: WARNING: Footnote [#] is not referenced. /build/reproducible-path/salmon-1.10.1+ds1/doc/source/salmon.rst:2: WARNING: Duplicate explicit target name: "here". /build/reproducible-path/salmon-1.10.1+ds1/doc/source/salmon.rst:2: WARNING: Duplicate explicit target name: "here". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 16%] alevin writing output... [ 33%] building writing output... [ 50%] file_formats writing output... [ 66%] index writing output... [ 83%] library_type writing output... [100%] salmon generating indices... genindex done writing additional pages... search done copying images... [100%] ReadLibraryIllustration.png copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 34 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="1.10.1+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-1.10.1+ds1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1' dh_auto_test --no-parallel cd obj-x86_64-linux-gnu && make -j1 test ARGS\+=--verbose ARGS\+=-j1 make[2]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j1 UpdateCTestConfiguration from :/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: unit_tests 1: Test command: /usr/bin/cmake "-DTOPLEVEL_DIR=/build/reproducible-path/salmon-1.10.1+ds1" "-P" "/build/reproducible-path/salmon-1.10.1+ds1/cmake/UnitTests.cmake" 1: Working Directory: /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src 1: Test timeout computed to be: 10000000 1: -- For unit tests, will set working directory to /build/reproducible-path/salmon-1.10.1+ds1/tests 1: =============================================================================== 1: All tests passed (2009183 assertions in 4 test cases) 1: 1/2 Test #1: unit_tests ....................... Passed 1.91 sec test 2 Start 2: salmon_read_test_quasi 2: Test command: /usr/bin/cmake "-DTOPLEVEL_DIR=/build/reproducible-path/salmon-1.10.1+ds1" "-P" "/build/reproducible-path/salmon-1.10.1+ds1/cmake/TestSalmonQuasi.cmake" 2: Working Directory: /build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu/src 2: Test timeout computed to be: 10000000 2: sample_data/ 2: sample_data/reads_2.fastq 2: sample_data/sample_alignments.bam 2: sample_data/transcripts.fasta 2: sample_data/reads_1.fastq 2: index ["sample_salmon_quasi_index"] did not previously exist . . . creating it 2: [2024-01-13 04:32:30.086] [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: [2024-01-13 04:32:30.086] [jLog] [info] building index 2: out : sample_salmon_quasi_index 2: [2024-01-13 04:32:30.086] [puff::index::jointLog] [info] Running fixFasta 2: 2: [Step 1 of 4] : counting k-mers 2: 2: [2024-01-13 04:32:30.106] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides 2: [2024-01-13 04:32:30.106] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts 2: wrote 15 cleaned references 2: [2024-01-13 04:32:30.106] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers 2: [2024-01-13 04:32:30.107] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20 2: Threads = 2 2: Vertex length = 31 2: Hash functions = 5 2: Filter size = 1048576 2: Capacity = 2 2: Files: 2: sample_salmon_quasi_index/ref_k31_fixed.fa 2: -------------------------------------------------------------------------------- 2: Round 0, 0:1048576 2: Pass Filling Filtering 2: 1 0 0 2: 2 0 0 2: True junctions count = 14 2: False junctions count = 17 2: Hash table size = 31 2: Candidate marks count = 54 2: -------------------------------------------------------------------------------- 2: Reallocating bifurcations time: 0 2: True marks count: 51 2: Edges construction time: 0 2: -------------------------------------------------------------------------------- 2: Distinct junctions = 14 2: 2: TwoPaCo::buildGraphMain:: allocated with scalable_malloc; freeing. 2: TwoPaCo::buildGraphMain:: Calling scalable_allocation_command(TBBMALLOC_CLEAN_ALL_BUFFERS, 0); 2: allowedIn: 12 2: Max Junction ID: 70 2: seen.size():569 kmerInfo.size():71 2: approximateContigTotalLength: 17465 2: counters for complex kmers: 2: (prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0 2: contig count: 24 element count: 19592 complex nodes: 0 2: # of ones in rank vector: 23 2: [2024-01-13 04:32:30.266] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file. 2: [2024-01-13 04:32:30.266] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory sample_salmon_quasi_index 2: size = 19592 2: ----------------------------------------- 2: | Loading contigs | Time = 80.638 us 2: ----------------------------------------- 2: size = 19592 2: ----------------------------------------- 2: | Loading contig boundaries | Time = 39.039 us 2: ----------------------------------------- 2: Number of ones: 23 2: Number of ones per inventory item: 512 2: Inventory entries filled: 1 2: 23 2: [2024-01-13 04:32:30.266] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure. 2: [2024-01-13 04:32:30.266] [puff::index::jointLog] [info] contig count for validation: 23 2: [2024-01-13 04:32:30.266] [puff::index::jointLog] [info] Total # of Contigs : 23 2: [2024-01-13 04:32:30.266] [puff::index::jointLog] [info] Total # of numerical Contigs : 23 2: [2024-01-13 04:32:30.266] [puff::index::jointLog] [info] Total # of contig vec entries: 36 2: [2024-01-13 04:32:30.266] [puff::index::jointLog] [info] bits per offset entry 6 2: [2024-01-13 04:32:30.266] [puff::index::jointLog] [info] Done constructing the contig vector. 24 2: [2024-01-13 04:32:30.266] [puff::index::jointLog] [info] # segments = 23 2: [2024-01-13 04:32:30.266] [puff::index::jointLog] [info] total length = 19,592 2: [2024-01-13 04:32:30.266] [puff::index::jointLog] [info] Reading the reference files ... 2: [2024-01-13 04:32:30.289] [puff::index::jointLog] [info] positional integer width = 15 2: [2024-01-13 04:32:30.289] [puff::index::jointLog] [info] seqSize = 19,592 2: [2024-01-13 04:32:30.289] [puff::index::jointLog] [info] rankSize = 19,592 2: [2024-01-13 04:32:30.289] [puff::index::jointLog] [info] edgeVecSize = 0 2: [2024-01-13 04:32:30.289] [puff::index::jointLog] [info] num keys = 18,902 2: [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 1 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 1 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 1 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 1 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 1 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 1 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 1 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 1 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 1 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 1 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 1 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 1 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 1 sec [Building BooPHF] 2.32 % elapsed: 0 min 0 sec remaining: 0 min 1 sec [Building 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elapsed: 0 min 1 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec [Building BooPHF] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec 2: [2024-01-13 04:32:30.809] [puff::index::jointLog] [info] mphf size = 0.0125198 MB 2: [2024-01-13 04:32:30.809] [puff::index::jointLog] [info] chunk size = 9,796 2: [2024-01-13 04:32:30.809] [puff::index::jointLog] [info] chunk 0 = [0, 9,796) 2: [2024-01-13 04:32:30.809] [puff::index::jointLog] [info] chunk 1 = [9,796, 19,562) 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: [2024-01-13 04:32:30.832] [puff::index::jointLog] [info] finished populating pos vector 2: [2024-01-13 04:32:30.832] [puff::index::jointLog] [info] writing index components 2: [2024-01-13 04:32:30.833] [puff::index::jointLog] [info] finished writing dense pufferfish index 2: [2024-01-13 04:32:30.833] [jLog] [info] done building index 2: ### salmon (selective-alignment-based) v1.10.1 2: ### [ program ] => salmon 2: ### [ command ] => quant 2: ### [ index ] => { sample_salmon_quasi_index } 2: ### [ libType ] => { IU } 2: ### [ mates1 ] => { reads_1.fastq } 2: ### [ mates2 ] => { reads_2.fastq } 2: ### [ output ] => { sample_salmon_quasi_quant } 2: Logs will be written to sample_salmon_quasi_quant/logs 2: ----------------------------------------- 2: | Loading contig table | Time = 21.573 us 2: ----------------------------------------- 2: size = 24 2: ----------------------------------------- 2: | Loading contig offsets | Time = 52.855 us 2: ----------------------------------------- 2: ----------------------------------------- 2: | Loading reference lengths | Time = 3.447 us 2: ----------------------------------------- 2: ----------------------------------------- 2: | Loading mphf table | Time = 52.236 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 = 90.507 us 2: ----------------------------------------- 2: size = 19592 2: ----------------------------------------- 2: | Loading sequence | Time = 42.131 us 2: ----------------------------------------- 2: size = 18902 2: ----------------------------------------- 2: | Loading positions | Time = 92.94 us 2: ----------------------------------------- 2: size = 28562 2: ----------------------------------------- 2: | Loading reference sequence | Time = 38.566 us 2: ----------------------------------------- 2: ----------------------------------------- 2: | Loading reference accumulative lengths | Time = 3.721 us 2: ----------------------------------------- 2: [2024-01-13 04:32:31.099] [jointLog] [info] setting maxHashResizeThreads to 15 2: [2024-01-13 04:32:31.099] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. 2: [2024-01-13 04:32:31.099] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 2: [2024-01-13 04:32:31.099] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35. 2: [2024-01-13 04:32:31.099] [jointLog] [info] parsing read library format 2: [2024-01-13 04:32:31.099] [jointLog] [info] There is 1 library. 2: [2024-01-13 04:32:31.099] [jointLog] [info] Loading pufferfish index 2: [2024-01-13 04:32:31.099] [jointLog] [info] Loading dense pufferfish index. 2: [2024-01-13 04:32:31.100] [jointLog] [info] done 2: 2: 2: 2: 2: [2024-01-13 04:32:31.454] [jointLog] [info] Index contained 15 targets 2: [2024-01-13 04:32:31.454] [jointLog] [info] Number of decoys : 0 2: 2: 2: 2: 2: 2: 2: 2: 2: [2024-01-13 04:32:32.186] [jointLog] [info] Computed 28 rich equivalence classes for further processing 2: [2024-01-13 04:32:32.186] [jointLog] [info] Counted 10,000 total reads in the equivalence classes 2: [2024-01-13 04:32:32.220] [jointLog] [info] Number of mappings discarded because of alignment score : 67 2: [2024-01-13 04:32:32.220] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0 2: [2024-01-13 04:32:32.220] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 2: [2024-01-13 04:32:32.220] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0 2: [2024-01-13 04:32:32.220] [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: [2024-01-13 04:32:32.220] [jointLog] [info] Mapping rate = 100% 2: 2: [2024-01-13 04:32:32.220] [jointLog] [info] finished quantifyLibrary() 2: [2024-01-13 04:32:32.221] [jointLog] [info] Starting optimizer 2: [2024-01-13 04:32:32.222] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate 2: [2024-01-13 04:32:32.222] [jointLog] [info] iteration = 0 | max rel diff. = 14.87 2: [2024-01-13 04:32:32.224] [jointLog] [info] iteration = 100 | max rel diff. = 2.94662e-05 2: [2024-01-13 04:32:32.224] [jointLog] [info] Finished optimizer 2: [2024-01-13 04:32:32.224] [jointLog] [info] writing output 2: 2: Salmon (read) ran successfully 2/2 Test #2: salmon_read_test_quasi ........... Passed 3.16 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 5.08 sec make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1' dh_auto_install cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/reproducible-path/salmon-1.10.1\+ds1/debian/salmon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/salmon-1.10.1+ds1 -B/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/libntcard.a -- Installing: /build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets.cmake -- Installing: /build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets-release.cmake -- Installing: /build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/libgraphdump.a -- Installing: /build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets.cmake -- Installing: /build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets-release.cmake -- Installing: /build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/libtwopaco.a -- Installing: /build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake -- Installing: /build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake -- Installing: /build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/bin/salmon -- Installing: /build/reproducible-path/salmon-1.10.1+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-1.10.1+ds1/obj-x86_64-linux-gnu' rm -Rvf /build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib removed '/build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/libsalmon_core.a' removed '/build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets-release.cmake' removed '/build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/twopaco/twopaco-targets.cmake' removed directory '/build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/twopaco' removed '/build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/libtwopaco.a' removed '/build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets-release.cmake' removed '/build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/graphdump/graphdump-targets.cmake' removed directory '/build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/graphdump' removed '/build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/libgraphdump.a' removed '/build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets-release.cmake' removed '/build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/ntcard/ntcard-targets.cmake' removed directory '/build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/ntcard' removed '/build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib/libntcard.a' removed directory '/build/reproducible-path/salmon-1.10.1+ds1/debian/salmon/usr/lib' make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.1+ds1' dh_install dh_installdocs dh_sphinxdoc dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/copybutton.js dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/menu.js dh_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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'salmon-dbgsym' in '../salmon-dbgsym_1.10.1+ds1-1_amd64.deb'. dpkg-deb: building package 'salmon' in '../salmon_1.10.1+ds1-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../salmon_1.10.1+ds1-1_amd64.buildinfo dpkg-genchanges --build=binary -O../salmon_1.10.1+ds1-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2339344 and its subdirectories I: Current time: Sat Jan 13 04:35:06 -12 2024 I: pbuilder-time-stamp: 1705163706