Diff of the two buildlogs: -- --- b1/build.log 2024-03-04 00:48:58.263321147 +0000 +++ b2/build.log 2024-03-04 00:57:22.931903117 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Mar 3 12:40:27 -12 2024 -I: pbuilder-time-stamp: 1709512827 +I: Current time: Sun Apr 6 21:12:02 +14 2025 +I: pbuilder-time-stamp: 1743923522 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./salmon_1.4.0+ds1-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.rm9oAT_8/trustedkeys.kbx': General error -gpgv: Signature made Thu Nov 26 06:34:33 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.R23VLVxr/trustedkeys.kbx': General error +gpgv: Signature made Fri Nov 27 08:34:33 2020 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./salmon_1.4.0+ds1-1.dsc @@ -32,135 +32,166 @@ dpkg-source: info: applying disable-version-check.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1715973/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1235706/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 6 21:12 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1235706/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1235706/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=12 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='505aa6deb9eb4a8d8c46b12a6f73e203' - 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='1715973' - PS1='# ' - PS2='> ' + INVOCATION_ID=986aef1888b541d78114392f0f391d7f + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1235706 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.Pd3jWQau/pbuilderrc_6OZP --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Pd3jWQau/b1 --logfile b1/build.log salmon_1.4.0+ds1-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.104:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Pd3jWQau/pbuilderrc_BCuf --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Pd3jWQau/b2 --logfile b2/build.log salmon_1.4.0+ds1-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.104:3128 I: uname -a - Linux codethink04-arm64 6.1.0-18-cloud-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-cloud-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux I: ls -l /bin total 5260 - -rwxr-xr-x 1 root root 1282512 Mar 27 2022 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 Jan 20 2022 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 64856 Jan 20 2022 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 182496 Jan 24 2023 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 93744 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 157864 Jan 20 2022 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Jan 20 2022 more - -rwsr-xr-x 1 root root 51360 Jan 20 2022 mount - -rwxr-xr-x 1 root root 14496 Jan 20 2022 mountpoint - -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Feb 6 21:23 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Jan 20 2022 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 543960 Jan 19 21:59 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Jan 20 2022 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Jan 20 2022 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 5898 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8049 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/1715973/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Mar 28 2022 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 Jan 21 2022 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 64856 Jan 21 2022 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 182496 Jan 25 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 93744 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 157864 Jan 21 2022 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Jan 21 2022 more + -rwsr-xr-x 1 root root 51360 Jan 21 2022 mount + -rwxr-xr-x 1 root root 14496 Jan 21 2022 mountpoint + -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 9 Apr 6 21:12 sh -> /bin/bash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Jan 21 2022 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 543960 Jan 20 2024 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Jan 21 2022 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 Jan 21 2022 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 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 5898 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 8049 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/1235706/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -425,7 +456,7 @@ Get: 167 http://deb.debian.org/debian bullseye/main arm64 python3-sphinx-rtd-theme all 0.5.1+dfsg-1 [20.9 kB] Get: 168 http://deb.debian.org/debian bullseye/main arm64 rapmap-dev all 0.15.0+dfsg-1 [194 kB] Get: 169 http://deb.debian.org/debian bullseye/main arm64 sphinx-doc all 3.4.3-2 [1971 kB] -Fetched 103 MB in 4s (27.8 MB/s) +Fetched 103 MB in 2s (63.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19702 files and directories currently installed.) @@ -1143,7 +1174,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/salmon-1.4.0+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_1.4.0+ds1-1_source.changes +I: user script /srv/workspace/pbuilder/1235706/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/1235706/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/salmon-1.4.0+ds1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../salmon_1.4.0+ds1-1_source.changes dpkg-buildpackage: info: source package salmon dpkg-buildpackage: info: source version 1.4.0+ds1-1 dpkg-buildpackage: info: source distribution unstable @@ -1283,9 +1318,9 @@ 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_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[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.4.0+ds1 /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/ntcard /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/DependInfo.cmake --color= -make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend make -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-1.4.0+ds1/obj-aarch64-linux-gnu' cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.4.0+ds1 /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/DependInfo.cmake --color= @@ -1297,147 +1332,130 @@ cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.4.0+ds1 /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake --color= make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.4.0+ds1 /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.4.0+ds1 /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.4.0+ds1 /build/reproducible-path/salmon-1.4.0+ds1/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.4.0+ds1 /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.4.0+ds1 /build/reproducible-path/salmon-1.4.0+ds1/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake --color= -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.4.0+ds1 /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend.internal". -Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend.internal". Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend.internal". Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/depend.internal". +Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend.internal". +Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend.internal". Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend.internal". -Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend.internal". Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend.internal". +Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/depend.internal". Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/depend.internal". -Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend.internal". -Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/depend.internal". +Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend.internal". +Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/depend.internal". Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend.internal". -Scanning dependencies of target ksw2pp_sse2 Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/depend.internal". Scanning dependencies of target ntcard +Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/alevin_core.dir/depend.internal". Scanning dependencies of target ksw2pp_sse4 +Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/alevin_core.dir/depend.internal". Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/depend.internal". Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/depend.internal". -make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build -make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/salmon_core.dir/depend.internal". +Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/salmon_core.dir/depend.internal". +Scanning dependencies of target ksw2pp_sse2 Scanning dependencies of target ksw2pp_basic -Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/alevin_core.dir/depend.internal". -Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/alevin_core.dir/depend.internal". +make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' make -f external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build.make external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/build make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/build -make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +make -f external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' Scanning dependencies of target graphdump -Scanning dependencies of target twopaco -Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/salmon_core.dir/depend.internal". -Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/salmon_core.dir/depend.internal". +make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +Scanning dependencies of target twopaco make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' make -f external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build.make external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/build -make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' make -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build -[ 1%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -[ 2%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -[ 3%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -[ 4%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -[ 5%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -[ 6%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c +make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +[ 1%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o +[ 2%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o +[ 4%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o +[ 3%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o +[ 5%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/kalloc.c cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -O3 -std=c++14 -o CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common/SignalHandler.cpp -[ 7%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -O3 -std=c++14 -o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common/Fcontrol.cpp -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -D__SSE4_1__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c +[ 6%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -D__SSE4_1__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -O3 -std=c++14 -o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common/Fcontrol.cpp +[ 7%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -O3 -std=c++14 -o CMakeFiles/ntcard.dir/nthll.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/nthll.cpp [ 8%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/graphdump.dir/graphdump.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/graphdump.cpp [ 9%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -Scanning dependencies of target alevin_core cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/dnachar.cpp +Scanning dependencies of target alevin_core make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/build -make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +[ 10%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o Scanning dependencies of target puffer +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/constructor.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -[ 9%] Building CXX object src/CMakeFiles/alevin_core.dir/edlib.cpp.o +make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' make -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/build -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/alevin_core.dir/edlib.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/edlib.cpp Scanning dependencies of target salmon_core -make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -[ 10%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +[ 10%] Building CXX object src/CMakeFiles/alevin_core.dir/edlib.cpp.o make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/build -[ 11%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndexer.cpp -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/Common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -O3 -std=c++14 -o CMakeFiles/ntcard.dir/nthll.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/ntcard/nthll.cpp +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/alevin_core.dir/edlib.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/edlib.cpp +make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -[ 12%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o +[ 11%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/jellyfish/mer_dna.cc +[ 12%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndexer.cpp [ 13%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extd.c -[ 14%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o +[ 14%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -D__SSE4_1__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c +[ 15%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp +[ 16%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp +[ 17%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extz.c -[ 16%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o -[ 16%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/constructor.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_gg.c -[ 17%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2.c [ 17%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -o CMakeFiles/salmon_core.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.4.0+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 -[ 18%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/SingleCellProtocols.cpp -[ 19%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o +[ 18%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/TranscriptGroup.cpp -[ 20%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2_sse.c -[ 20%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp -[ 21%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp -In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/../common/streamfastaparser.h:8, - from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/graphdump.cpp:18: -/usr/include/tbb/mutex.h:21:140: note: '#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' - 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") - | ^ -[ 22%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/AlevinUtils.cpp -make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -[ 23%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -D__SSE4_1__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c -[ 23%] Built target ksw2pp_sse2 +[ 19%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/SingleCellProtocols.cpp +[ 20%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_gg.c In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:12, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/assemblyedgeconstructor.h:4, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp:20: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ -[ 24%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/EffectiveLengthStats.cpp -[ 25%] Linking CXX static library libntcard.a -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake -[ 26%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-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-1.4.0+ds1/obj-aarch64-linux-gnu' -[ 26%] Built target ntcard +In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/../common/streamfastaparser.h:8, + from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphdump/graphdump.cpp:18: +/usr/include/tbb/mutex.h:21:140: note: '#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' + 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") + | ^ +[ 21%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o +[ 22%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/test.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:13, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/assemblyedgeconstructor.h:4, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp:20: @@ -1450,60 +1468,58 @@ /usr/include/tbb/compat/thread:21:146: note: '#pragma message: TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ -[ 27%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/LibraryFormat.cpp +[ 23%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2.c +[ 24%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:19, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/assemblyedgeconstructor.h:4, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp:20: /usr/include/tbb/task_scheduler_init.h:21:154: note: '#pragma message: TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ -[ 28%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -D__SSE4_1__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c -[ 29%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp +[ 25%] Linking CXX static library libntcard.a +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -[ 29%] Built target ksw2pp_basic -[ 30%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/VersionChecker.cpp -[ 31%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/GenomicFeature.cpp -[ 32%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/test.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp -[ 33%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SBModel.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/SBModel.cpp +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -E cmake_link_script CMakeFiles/ntcard.dir/link.txt --verbose=1 +[ 26%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp +/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 +[ 26%] Built target ksw2pp_sse4 +/usr/bin/ranlib libntcard.a +make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +[ 26%] Built target ntcard +[ 27%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp +[ 28%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/common.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/common.cpp +[ 29%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.h:8, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp:4: /usr/include/tbb/mutex.h:21:140: note: '#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2_sse.c +[ 30%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c +[ 31%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/EffectiveLengthStats.cpp +[ 32%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/AlevinUtils.cpp In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:12, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp:11: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ -make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -[ 33%] Built target ksw2pp_sse4 -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-1.4.0+ds1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.4.0+ds1 /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend.internal". -Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend.internal". -Scanning dependencies of target ksw2pp -make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/build -make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -[ 34%] Linking CXX static library libksw2pp.a -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 -"/usr/bin/gcc-ar-10" 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 -[ 35%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -"/usr/bin/gcc-ranlib-10" libksw2pp.a -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp -make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -[ 35%] Built target ksw2pp -[ 36%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp +In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:12, + from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp:11: +/usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' + 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") + | ^ +[ 33%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp +[ 33%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:13, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp:11: /usr/include/tbb/mutex.h:21:140: note: '#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' @@ -1514,20 +1530,13 @@ /usr/include/tbb/compat/thread:21:146: note: '#pragma message: TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/compat/thread is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ +[ 34%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndex.cpp In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:19, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp:11: /usr/include/tbb/task_scheduler_init.h:21:154: note: '#pragma message: TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ -[ 37%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/FastxParser.cpp -[ 38%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -std=c++14 -o CMakeFiles/twopaco.dir/common.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/common.cpp -In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:12, - from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp:11: -/usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' - 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") - | ^ In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h:13, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp:11: /usr/include/tbb/mutex.h:21:140: note: '#pragma message: TBB Warning: tbb/mutex.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' @@ -1543,12 +1552,34 @@ /usr/include/tbb/task_scheduler_init.h:21:154: note: '#pragma message: TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is deprecated. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ -[ 39%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/StadenUtils.cpp -[ 40%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/SalmonUtils.cpp -[ 41%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/DistributionUtils.cpp +make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +[ 34%] Built target ksw2pp_sse2 +[ 35%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp +make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +[ 35%] 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-1.4.0+ds1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.4.0+ds1 /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend.internal". +Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp.dir/depend.internal". +Scanning dependencies of target ksw2pp +make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +make -f external/pufferfish/src/CMakeFiles/ksw2pp.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp.dir/build +make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +[ 36%] Linking CXX static library libksw2pp.a +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 +"/usr/bin/gcc-ar-10" 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-10" libksw2pp.a +[ 37%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/LibraryFormat.cpp +make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +[ 37%] Built target ksw2pp +[ 38%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/GenomicFeature.cpp +[ 39%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/VersionChecker.cpp In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20: @@ -1589,45 +1620,49 @@ /build/reproducible-path/salmon-1.4.0+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); | ^~~~~~~~ -[ 42%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp -[ 43%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o +[ 40%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SBModel.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/SBModel.cpp +[ 41%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/FastxParser.cpp +[ 42%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/StadenUtils.cpp +[ 43%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/SalmonUtils.cpp +[ 44%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/DistributionUtils.cpp +[ 45%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/SalmonExceptions.cpp -[ 44%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o +[ 46%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/SalmonStringUtils.cpp -[ 45%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o +[ 47%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -std=c++14 -o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/SimplePosBias.cpp -[ 46%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o +[ 48%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 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/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/rank9b.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/rank9b.cpp @@ -1641,32 +1676,8 @@ cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishExamine.cpp [ 60%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/FastxParser.cpp -[ 61%] Linking CXX static library libalevin_core.a -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 -"/usr/bin/gcc-ar-10" 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 -"/usr/bin/gcc-ranlib-10" libalevin_core.a -make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -[ 61%] Built target alevin_core -[ 62%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o +[ 61%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp -[ 63%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferFS.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferFS.cpp -[ 64%] Building C object external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -o CMakeFiles/puffer.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/xxhash.c -cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C -[ 65%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp -[ 66%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/MemCollector.cpp -[ 66%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/MemChainer.cpp -[ 67%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PuffAligner.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PuffAligner.cpp -[ 68%] Linking CXX static library libsalmon_core.a -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1 -"/usr/bin/gcc-ar-10" cr libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.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 In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1: /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::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 > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]': @@ -1703,24 +1714,28 @@ /build/reproducible-path/salmon-1.4.0+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); | ^~~~~~~~ -[ 69%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishAligner.cpp -"/usr/bin/gcc-ranlib-10" libsalmon_core.a -make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -[ 69%] Built target salmon_core -make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/depend -make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.4.0+ds1 /build/reproducible-path/salmon-1.4.0+ds1/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/unitTests.dir/DependInfo.cmake --color= -Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/unitTests.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/unitTests.dir/depend.internal". -Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/unitTests.dir/depend.internal". -Scanning dependencies of target unitTests +[ 62%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferFS.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferFS.cpp +[ 63%] Building C object external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -o CMakeFiles/puffer.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/xxhash.c +cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C +[ 64%] Linking CXX static library libalevin_core.a +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 +"/usr/bin/gcc-ar-10" 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 +"/usr/bin/gcc-ranlib-10" libalevin_core.a make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/build -make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -[ 70%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -pthread -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 -o CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/tests/UnitTests.cpp -[ 71%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/RefSeqConstructor.cpp +[ 64%] Built target alevin_core +[ 65%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp +[ 66%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/MemCollector.cpp +[ 66%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/MemChainer.cpp +[ 67%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PuffAligner.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PuffAligner.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PuffAligner.cpp +[ 68%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/PufferfishAligner.cpp In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/FixFasta.cpp:4: /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::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 > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >; spp::sparse_hashtable::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-1.4.0+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 > > >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator > >, spp::sparsegroup > >, spp::libc_allocator > > > >*, std::pair > >*, std::input_iterator_tag, spp::libc_allocator > > > >]' @@ -1753,12 +1768,34 @@ /build/reproducible-path/salmon-1.4.0+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); | ^~~~~~~~ +[ 69%] Linking CXX static library libsalmon_core.a +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1 +"/usr/bin/gcc-ar-10" cr libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.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-10" libsalmon_core.a +make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +[ 69%] Built target salmon_core +make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/depend +make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.4.0+ds1 /build/reproducible-path/salmon-1.4.0+ds1/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/unitTests.dir/DependInfo.cmake --color= +Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/unitTests.dir/DependInfo.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/unitTests.dir/depend.internal". +Dependee "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/unitTests.dir/depend.internal". +Scanning dependencies of target unitTests +make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/build +make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' +[ 70%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -pthread -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 -o CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/tests/UnitTests.cpp +[ 71%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/RefSeqConstructor.cpp [ 72%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/metro/metrohash64.cpp [ 73%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -I/build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.4.0+ds1/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -std=c++14 -o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/LibraryFormat.cpp [ 74%] Building CXX object src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -pthread -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 -o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/FragmentLengthDistribution.cpp +[ 75%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -pthread -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 -o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/install/src/pufferfish/rank9b.cpp In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include/RefSeqConstructor.hpp:5, from /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/src/RefSeqConstructor.cpp:1: /build/reproducible-path/salmon-1.4.0+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable::destructive_iterator spp::sparse_hashtable::_mk_destructive_iterator(spp::sparse_hashtable::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 >; spp::sparse_hashtable::destructive_iterator = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >; spp::sparse_hashtable::dest_it = spp::Two_d_destructive_iterator, spp::sparsegroup, spp::libc_allocator > >*, std::pair*, std::input_iterator_tag, spp::libc_allocator > >]': @@ -1778,8 +1815,6 @@ /build/reproducible-path/salmon-1.4.0+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); | ^~~~~~~~ -[ 75%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -pthread -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 -o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/external/install/src/pufferfish/rank9b.cpp [ 76%] Linking CXX static library libpuffer.a cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -P CMakeFiles/puffer.dir/cmake_clean_target.cmake cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/puffer.dir/link.txt --verbose=1 @@ -1810,30 +1845,30 @@ make[4]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/build make[4]: Entering directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' -[ 79%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/CollapsedEMOptimizer.cpp +[ 79%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/CollapsedCellOptimizer.cpp [ 80%] Building CXX object src/CMakeFiles/salmon.dir/EMUtils.cpp.o -[ 81%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o -[ 82%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o +[ 81%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/EMUtils.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/EMUtils.cpp [ 83%] Building CXX object src/CMakeFiles/salmon.dir/Salmon.cpp.o +[ 83%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o [ 84%] Building CXX object src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/CollapsedCellOptimizer.cpp -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/EMUtils.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/EMUtils.cpp -[ 85%] Building CXX object src/CMakeFiles/salmon.dir/DedupUMI.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/CollapsedEMOptimizer.cpp cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/Salmon.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/Salmon.cpp -[ 86%] Building CXX object src/CMakeFiles/salmon.dir/Alevin.cpp.o +[ 85%] Building CXX object src/CMakeFiles/salmon.dir/Graph.cpp.o +[ 86%] Building CXX object src/CMakeFiles/salmon.dir/DedupUMI.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/CollapsedGibbsSampler.cpp -[ 87%] Building CXX object src/CMakeFiles/salmon.dir/Graph.cpp.o -[ 87%] Building CXX object src/CMakeFiles/salmon.dir/AlevinHash.cpp.o +[ 87%] Building CXX object src/CMakeFiles/salmon.dir/Alevin.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/BuildSalmonIndex.cpp -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/DedupUMI.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/DedupUMI.cpp +[ 87%] Building CXX object src/CMakeFiles/salmon.dir/AlevinHash.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/Graph.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/Graph.cpp +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/DedupUMI.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/DedupUMI.cpp +[ 88%] Building CXX object src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type 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-fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/AlevinHash.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/AlevinHash.cpp -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 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-I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/SalmonAlevin.cpp +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/WhiteList.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/WhiteList.cpp In file included from /build/reproducible-path/salmon-1.4.0+ds1/include/pcg_random.hpp:104, from /build/reproducible-path/salmon-1.4.0+ds1/src/CollapsedGibbsSampler.cpp:23: /build/reproducible-path/salmon-1.4.0+ds1/include/pcg_extras.hpp:563:51: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] @@ -2020,8 +2055,6 @@ /build/reproducible-path/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -[ 95%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/ProgramOptionsGenerator.cpp /build/reproducible-path/salmon-1.4.0+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-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1909:23: 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]' @@ -2034,43 +2067,8 @@ /build/reproducible-path/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:65, - from /build/reproducible-path/salmon-1.4.0+ds1/include/AlevinUtils.hpp:46, - from /build/reproducible-path/salmon-1.4.0+ds1/include/Graph.hpp:8, - from /build/reproducible-path/salmon-1.4.0+ds1/include/DedupUMI.hpp:4, - from /build/reproducible-path/salmon-1.4.0+ds1/src/DedupUMI.cpp:1: -/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h: In instantiation of 'T* spp::libc_allocator::reallocate(spp::libc_allocator::pointer, size_t) [with T = std::pair, unsigned int>; spp::libc_allocator::pointer = std::pair, unsigned int>*; size_t = long unsigned int]': -/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1383:38: required from 'void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]' -/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char]' -/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::pointer = std::pair, unsigned int>*; spp::sparsegroup::value_type = std::pair, unsigned int>; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char]' -/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from 'void spp::sparsetable::move(spp::sparsetable::size_type, spp::sparsetable::reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsetable::size_type = long unsigned int; spp::sparsetable::reference = std::pair, unsigned int>&; spp::sparsetable::value_type = std::pair, unsigned int>]' -/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, 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> >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, 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> >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/reproducible-path/salmon-1.4.0+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-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from 'void spp::sparse_hashtable::resize(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> >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:3795:51: required from 'void spp::sparse_hash_map::resize(spp::sparse_hash_map::size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hash_map::size_type = long unsigned int]' -/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:3797:41: required from 'void spp::sparse_hash_map::reserve(spp::sparse_hash_map::size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hash_map::size_type = long unsigned int]' -/build/reproducible-path/salmon-1.4.0+ds1/src/DedupUMI.cpp:39:36: required from here -/build/reproducible-path/salmon-1.4.0+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++/10/bits/stl_algobase.h:64, - from /usr/include/c++/10/bits/char_traits.h:39, - from /usr/include/c++/10/string:40, - from /usr/include/c++/10/bits/locale_classes.h:40, - from /usr/include/c++/10/bits/ios_base.h:41, - from /usr/include/c++/10/streambuf:41, - from /usr/include/c++/10/bits/streambuf_iterator.h:35, - from /usr/include/c++/10/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-1.4.0+ds1/include/Graph.hpp:4, - from /build/reproducible-path/salmon-1.4.0+ds1/include/DedupUMI.hpp:4, - from /build/reproducible-path/salmon-1.4.0+ds1/src/DedupUMI.cpp:1: -/usr/include/c++/10/bits/stl_pair.h:211:12: note: 'struct std::pair, unsigned int>' declared here - 211 | struct pair - | ^~~~ +[ 95%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o +cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/ProgramOptionsGenerator.cpp /build/reproducible-path/salmon-1.4.0+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-1.4.0+ds1/src/SalmonAlevin.cpp:1886:33: required from 'sc_align_read_library:: [with auto:1 = fastx_parser::FastxParser; auto:2 = PufferfishSparseIndex; size_t = long unsigned int]' /build/reproducible-path/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:1907:23: 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]' @@ -2191,6 +2189,43 @@ /build/reproducible-path/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:388:63: warning: unused parameter 'transcripts' [-Wunused-parameter] 388 | IndexT* qidx, std::vector& transcripts, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:65, + from /build/reproducible-path/salmon-1.4.0+ds1/include/AlevinUtils.hpp:46, + from /build/reproducible-path/salmon-1.4.0+ds1/include/Graph.hpp:8, + from /build/reproducible-path/salmon-1.4.0+ds1/include/DedupUMI.hpp:4, + from /build/reproducible-path/salmon-1.4.0+ds1/src/DedupUMI.cpp:1: +/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp_utils.h: In instantiation of 'T* spp::libc_allocator::reallocate(spp::libc_allocator::pointer, size_t) [with T = std::pair, unsigned int>; spp::libc_allocator::pointer = std::pair, unsigned int>*; size_t = long unsigned int]': +/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1383:38: required from 'void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]' +/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1435:21: required from 'void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char]' +/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:1453:13: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair, unsigned int>; T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsegroup::pointer = std::pair, unsigned int>*; spp::sparsegroup::value_type = std::pair, unsigned int>; spp::sparsegroup::allocator_type = spp::libc_allocator, unsigned int> >; spp::sparsegroup::size_type = unsigned char]' +/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2251:27: required from 'void spp::sparsetable::move(spp::sparsetable::size_type, spp::sparsetable::reference) [with T = std::pair, unsigned int>; Alloc = spp::libc_allocator, unsigned int> >; spp::sparsetable::size_type = long unsigned int; spp::sparsetable::reference = std::pair, unsigned int>&; spp::sparsetable::value_type = std::pair, unsigned int>]' +/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2830:23: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, 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> >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2948:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, 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> >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/reproducible-path/salmon-1.4.0+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-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:2846:13: required from 'void spp::sparse_hashtable::resize(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> >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:3795:51: required from 'void spp::sparse_hash_map::resize(spp::sparse_hash_map::size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hash_map::size_type = long unsigned int]' +/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/sparsepp/spp.h:3797:41: required from 'void spp::sparse_hash_map::reserve(spp::sparse_hash_map::size_type) [with Key = std::pair; T = unsigned int; HashFcn = boost::hash >; EqualKey = std::equal_to >; Alloc = spp::libc_allocator, unsigned int> >; spp::sparse_hash_map::size_type = long unsigned int]' +/build/reproducible-path/salmon-1.4.0+ds1/src/DedupUMI.cpp:39:36: required from here +/build/reproducible-path/salmon-1.4.0+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++/10/bits/stl_algobase.h:64, + from /usr/include/c++/10/bits/char_traits.h:39, + from /usr/include/c++/10/string:40, + from /usr/include/c++/10/bits/locale_classes.h:40, + from /usr/include/c++/10/bits/ios_base.h:41, + from /usr/include/c++/10/streambuf:41, + from /usr/include/c++/10/bits/streambuf_iterator.h:35, + from /usr/include/c++/10/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-1.4.0+ds1/include/Graph.hpp:4, + from /build/reproducible-path/salmon-1.4.0+ds1/include/DedupUMI.hpp:4, + from /build/reproducible-path/salmon-1.4.0+ds1/src/DedupUMI.cpp:1: +/usr/include/c++/10/bits/stl_pair.h:211:12: note: 'struct std::pair, unsigned int>' declared here + 211 | struct pair + | ^~~~ [ 96%] Building CXX object src/CMakeFiles/salmon.dir/FASTAParser.cpp.o cd /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.4.0+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.4.0+ds1/external -I/build/reproducible-path/salmon-1.4.0+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.4.0+ds1/external/install/include/pufferfish/digestpp -g -O2 -fdebug-prefix-map=/build/reproducible-path/salmon-1.4.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto -fno-fat-lto-objects -fsigned-char -pthread -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -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 -o CMakeFiles/salmon.dir/FASTAParser.cpp.o -c /build/reproducible-path/salmon-1.4.0+ds1/src/FASTAParser.cpp [ 97%] Building CXX object src/CMakeFiles/salmon.dir/AlignmentModel.cpp.o @@ -2369,13 +2404,13 @@ /usr/bin/ctest --force-new-ctest-process -j1 Test project /build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu Start 1: unit_tests -1/2 Test #1: unit_tests ....................... Passed 0.27 sec +1/2 Test #1: unit_tests ....................... Passed 0.26 sec Start 2: salmon_read_test_quasi -2/2 Test #2: salmon_read_test_quasi ........... Passed 0.92 sec +2/2 Test #2: salmon_read_test_quasi ........... Passed 0.90 sec 100% tests passed, 0 tests failed out of 2 -Total Test time (real) = 1.21 sec +Total Test time (real) = 1.16 sec make[2]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1/obj-aarch64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/salmon-1.4.0+ds1' create-stamp debian/debhelper-build-stamp @@ -2447,8 +2482,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'salmon-dbgsym' in '../salmon-dbgsym_1.4.0+ds1-1_arm64.deb'. dpkg-deb: building package 'salmon' in '../salmon_1.4.0+ds1-1_arm64.deb'. +dpkg-deb: building package 'salmon-dbgsym' in '../salmon-dbgsym_1.4.0+ds1-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../salmon_1.4.0+ds1-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2456,12 +2491,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1235706/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1235706/tmp/hooks/B01_cleanup finished 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/1715973 and its subdirectories -I: Current time: Sun Mar 3 12:48:57 -12 2024 -I: pbuilder-time-stamp: 1709513337 +I: removing directory /srv/workspace/pbuilder/1235706 and its subdirectories +I: Current time: Sun Apr 6 21:20:21 +14 2025 +I: pbuilder-time-stamp: 1743924021