Diff of the two buildlogs: -- --- b1/build.log 2020-07-30 02:35:18.193146856 +0000 +++ b2/build.log 2020-07-30 02:40:41.191163165 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jul 29 14:32:55 -12 2020 -I: pbuilder-time-stamp: 1596076375 +I: Current time: Wed Sep 1 22:58:29 +14 2021 +I: pbuilder-time-stamp: 1630486709 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Tue Jan 1 23:07:29 2019 -12 +gpgv: Signature made Thu Jan 3 01:07:29 2019 +14 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rapmap_0.12.0+dfsg-3.dsc @@ -33,136 +33,170 @@ dpkg-source: info: applying no_gomp_needed I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/30864/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/27180/tmp/hooks/D01_modify_environment starting +debug: Running on codethink-sled9-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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/27180/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/27180/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - 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]="0" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + 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 parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='30864' - PS1='# ' - PS2='> ' + 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=27180 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/tmp.0FTTmsYmFN/pbuilderrc_HvfJ --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.0FTTmsYmFN/b1 --logfile b1/build.log rapmap_0.12.0+dfsg-3.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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/tmp.0FTTmsYmFN/pbuilderrc_93Wh --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.0FTTmsYmFN/b2 --logfile b2/build.log rapmap_0.12.0+dfsg-3.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink-sled12-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 - -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash - -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat - -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown - -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp - -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash - -rwxr-xr-x 1 root root 97136 Feb 28 2019 date - -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93752 Feb 28 2019 df - -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir - -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 27256 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34824 Apr 22 07:38 fusermount - -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln - -rwxr-xr-x 1 root root 52544 Jul 26 2018 login - -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 38840 Jan 9 2019 more - -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm - -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 27 20:26 sh -> dash - -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty - -rwsr-xr-x 1 root root 59424 Jan 9 2019 su - -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync - -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar - -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch - -rwxr-xr-x 1 root root 27256 Feb 28 2019 true - -rwxr-xr-x 1 root root 14264 Apr 22 07:38 ulockmgr_server - -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount - -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/30864/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1216928 Apr 18 2019 bash + -rwxr-xr-x 3 root root 34808 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 34808 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 34808 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14264 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 35576 Mar 1 2019 cat + -rwxr-xr-x 1 root root 60256 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 56096 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 64368 Mar 1 2019 chown + -rwxr-xr-x 1 root root 134632 Mar 1 2019 cp + -rwxr-xr-x 1 root root 129536 Jan 18 2019 dash + -rwxr-xr-x 1 root root 97136 Mar 1 2019 date + -rwxr-xr-x 1 root root 76736 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93752 Mar 1 2019 df + -rwxr-xr-x 1 root root 138848 Mar 1 2019 dir + -rwxr-xr-x 1 root root 75984 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 31368 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 27256 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68792 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34824 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 174304 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 89656 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 18440 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 64472 Mar 1 2019 ln + -rwxr-xr-x 1 root root 52544 Jul 27 2018 login + -rwxr-xr-x 1 root root 138848 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108552 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 76840 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 64480 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 39736 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 38840 Jan 10 2019 more + -rwsr-xr-x 1 root root 47112 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14344 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138736 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35560 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 43712 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68440 Mar 1 2019 rm + -rwxr-xr-x 1 root root 39624 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 19144 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 1 22:58 sh -> bash + lrwxrwxrwx 1 root root 4 Aug 31 04:48 sh.distrib -> dash + -rwxr-xr-x 1 root root 31384 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 72480 Mar 1 2019 stty + -rwsr-xr-x 1 root root 59424 Jan 10 2019 su + -rwxr-xr-x 1 root root 31416 Mar 1 2019 sync + -rwxr-xr-x 1 root root 449416 Apr 24 2019 tar + -rwxr-xr-x 1 root root 10560 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 88968 Mar 1 2019 touch + -rwxr-xr-x 1 root root 27256 Mar 1 2019 true + -rwxr-xr-x 1 root root 14264 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 30728 Jan 10 2019 umount + -rwxr-xr-x 1 root root 31384 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138848 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34824 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/27180/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -305,7 +339,7 @@ Get: 83 http://deb.debian.org/debian buster/main arm64 python-pkg-resources all 40.8.0-1 [182 kB] Get: 84 http://deb.debian.org/debian buster/main arm64 python-markdown all 3.0.1-3 [60.6 kB] Get: 85 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] -Fetched 33.5 MB in 8s (4263 kB/s) +Fetched 33.5 MB in 2s (15.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) @@ -671,7 +705,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/rapmap-0.12.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/rapmap-0.12.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package rapmap dpkg-buildpackage: info: source version 0.12.0+dfsg-3 dpkg-buildpackage: info: source distribution unstable @@ -755,22 +789,22 @@ make[4]: Leaving directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/rapmap.dir/build.make src/CMakeFiles/rapmap.dir/build make[4]: Entering directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' -[ 15%] Building CXX object src/CMakeFiles/rapmap.dir/RapMap.cpp.o +[ 7%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapUtils.cpp.o +cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapUtils.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapUtils.cpp [ 15%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o -cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMap.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMap.cpp cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapSAIndexer.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp -[ 23%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o +[ 23%] Building CXX object src/CMakeFiles/rapmap.dir/RapMap.cpp.o +cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMap.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMap.cpp +[ 30%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapSAMapper.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp -[ 30%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapUtils.cpp.o -cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapUtils.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapUtils.cpp -[ 46%] Building CXX object src/CMakeFiles/rapmap.dir/FastxParser.cpp.o -[ 46%] Building CXX object src/CMakeFiles/rapmap.dir/HitManager.cpp.o -cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/HitManager.cpp.o -c /build/rapmap-0.12.0+dfsg/src/HitManager.cpp -cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/FastxParser.cpp.o -c /build/rapmap-0.12.0+dfsg/src/FastxParser.cpp -[ 61%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o -[ 53%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o +[ 38%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o +[ 46%] Building CXX object src/CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapFileSystem.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapFileSystem.cpp cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/RapMapSAIndex.cpp.o -c /build/rapmap-0.12.0+dfsg/src/RapMapSAIndex.cpp +[ 53%] Building CXX object src/CMakeFiles/rapmap.dir/HitManager.cpp.o +[ 61%] Building CXX object src/CMakeFiles/rapmap.dir/FastxParser.cpp.o +cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/FastxParser.cpp.o -c /build/rapmap-0.12.0+dfsg/src/FastxParser.cpp +cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/HitManager.cpp.o -c /build/rapmap-0.12.0+dfsg/src/HitManager.cpp [ 69%] Building CXX object src/CMakeFiles/rapmap.dir/rank9b.cpp.o cd /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/rapmap-0.12.0+dfsg/include -I/build/rapmap-0.12.0+dfsg/digestpp -I/build/rapmap-0.12.0+dfsg/external -I/build/rapmap-0.12.0+dfsg/external/cereal/include -I/build/rapmap-0.12.0+dfsg/external/install/include -g -O2 -ffile-prefix-map=/build/rapmap-0.12.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -funroll-loops -fPIC -fomit-frame-pointer -O4 -DHAVE_ANSI_TERM -Wall -Wno-unused-function -Wno-unused-local-typedef -std=c++14 -static-libstdc++ -Wno-unknown-pragmas -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -o CMakeFiles/rapmap.dir/rank9b.cpp.o -c /build/rapmap-0.12.0+dfsg/src/rank9b.cpp [ 76%] Building CXX object src/CMakeFiles/rapmap.dir/stringpiece.cc.o @@ -944,70 +978,6 @@ class sparsegroup ^~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::size_type = long unsigned int]': -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = int; spp::sparse_hash_map::key_type = int]' -/build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:162:11: required from 'bool buildPerfectHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:777:41: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] - memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} declared here - class sparsegroup - ^~~~~~~~~~~ -In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]': -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1431:13: required from 'void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1449:9: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::pointer = std::pair*; spp::sparsegroup::value_type = std::pair; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2241:17: required from 'spp::sparsetable::value_type& spp::sparsetable::set(spp::sparsetable::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::reference = std::pair&; spp::sparsetable::value_type = std::pair; spp::sparsetable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3171:34: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, spp::sparse_hashtable::size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::reference = std::pair&; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3280:81: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = long int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long int; T = long int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = long int; spp::sparse_hash_map::key_type = long int]' -/build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:162:11: required from 'bool buildPerfectHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = long int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:756:41: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1384:19: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] - memcpy(_group + i, _group + i-1, sizeof(*_group)); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/utility:70, - from /usr/include/c++/8/algorithm:60, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:22: -/usr/include/c++/8/bits/stl_pair.h:208:12: note: 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} declared here - struct pair - ^~~~ -In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]': -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1431:13: required from 'void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1449:9: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::pointer = std::pair*; spp::sparsegroup::value_type = std::pair; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2241:17: required from 'spp::sparsetable::value_type& spp::sparsetable::set(spp::sparsetable::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::reference = std::pair&; spp::sparsetable::value_type = std::pair; spp::sparsetable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3171:34: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, spp::sparse_hashtable::size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::reference = std::pair&; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::size_type = long unsigned int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3280:81: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = int]' -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = int; spp::sparse_hash_map::key_type = int]' -/build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:162:11: required from 'bool buildPerfectHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:777:41: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' -/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here -/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1384:19: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] - memcpy(_group + i, _group + i-1, sizeof(*_group)); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/utility:70, - from /usr/include/c++/8/algorithm:60, - from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:22: -/usr/include/c++/8/bits/stl_pair.h:208:12: note: 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} declared here - struct pair - ^~~~ -In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/HitManager.hpp:25, from /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::size_type = long unsigned int]': @@ -1056,6 +1026,26 @@ class sparsegroup ^~~~~~~~~~~ In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsetable::resize(spp::sparsetable::size_type) [with T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::size_type = long unsigned int]': +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2805:13: required from 'void spp::sparse_hashtable::_move_from(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2949:9: required from 'spp::sparse_hashtable::sparse_hashtable(spp::sparse_hashtable::MoveDontCopyT, spp::sparse_hashtable&, spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2744:26: required from 'bool spp::sparse_hashtable::_resize_delta(spp::sparse_hashtable::size_type) [with Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3269:21: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = int; spp::sparse_hash_map::key_type = int]' +/build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:162:11: required from 'bool buildPerfectHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:777:41: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2090:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] + memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz)); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1027:7: note: 'spp::sparsetable, spp::libc_allocator > >::group_type' {aka 'class spp::sparsegroup, spp::libc_allocator > >'} declared here + class sparsegroup + ^~~~~~~~~~~ +In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, from /build/rapmap-0.12.0+dfsg/include/HitManager.hpp:25, from /build/rapmap-0.12.0+dfsg/src/RapMapSAMapper.cpp:50: /build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]': @@ -1109,6 +1099,50 @@ /usr/include/c++/8/bits/stl_pair.h:208:12: note: 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} declared here struct pair ^~~~ +In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]': +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1431:13: required from 'void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1449:9: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::pointer = std::pair*; spp::sparsegroup::value_type = std::pair; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2241:17: required from 'spp::sparsetable::value_type& spp::sparsetable::set(spp::sparsetable::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::reference = std::pair&; spp::sparsetable::value_type = std::pair; spp::sparsetable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3171:34: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, spp::sparse_hashtable::size_type, bool) [with T = std::pair; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::reference = std::pair&; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3280:81: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = long int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = long int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = long int; T = long int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = long int; spp::sparse_hash_map::key_type = long int]' +/build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:162:11: required from 'bool buildPerfectHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = long int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:756:41: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1384:19: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] + memcpy(_group + i, _group + i-1, sizeof(*_group)); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/utility:70, + from /usr/include/c++/8/algorithm:60, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:22: +/usr/include/c++/8/bits/stl_pair.h:208:12: note: 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} declared here + struct pair + ^~~~ +In file included from /build/rapmap-0.12.0+dfsg/include/RapMapUtils.hpp:29, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:50: +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h: In instantiation of 'void spp::sparsegroup::_set_aux(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&, spp::sparsegroup::realloc_ok_type) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char; spp::sparsegroup::realloc_ok_type = spp::integral_constant]': +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1431:13: required from 'void spp::sparsegroup::_set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1449:9: required from 'spp::sparsegroup::value_type* spp::sparsegroup::set(spp::sparsegroup::allocator_type&, spp::sparsegroup::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsegroup::pointer = std::pair*; spp::sparsegroup::value_type = std::pair; spp::sparsegroup::allocator_type = spp::libc_allocator >; spp::sparsegroup::size_type = unsigned char]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:2241:17: required from 'spp::sparsetable::value_type& spp::sparsetable::set(spp::sparsetable::size_type, Val&) [with Val = std::pair; T = std::pair; Alloc = spp::libc_allocator >; spp::sparsetable::reference = std::pair&; spp::sparsetable::value_type = std::pair; spp::sparsetable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3171:34: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::_insert_at(T&, spp::sparse_hashtable::size_type, bool) [with T = std::pair; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::reference = std::pair&; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::size_type = long unsigned int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3280:81: required from 'spp::sparse_hashtable::value_type& spp::sparse_hashtable::find_or_insert(const key_type&) [with DefaultValue = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::DefaultValue; Value = std::pair; Key = int; HashFcn = spp::spp_hash; ExtractKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SelectKey; SetKey = spp::sparse_hash_map, std::equal_to, spp::libc_allocator > >::SetKey; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hashtable::value_type = std::pair; spp::sparse_hashtable::key_type = int]' +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:3792:63: required from 'spp::sparse_hash_map::mapped_type& spp::sparse_hash_map::operator[](const key_type&) [with Key = int; T = int; HashFcn = spp::spp_hash; EqualKey = std::equal_to; Alloc = spp::libc_allocator >; spp::sparse_hash_map::mapped_type = int; spp::sparse_hash_map::key_type = int]' +/build/rapmap-0.12.0+dfsg/include/FrugalBooMap.hpp:106:22: required from 'void FrugalBooMap::add(KeyT&&, ValueT&&) [with KeyT = long unsigned int; ValueT = rapmap::utils::SAInterval]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:162:11: required from 'bool buildPerfectHash(const string&, nonstd::sv_lite::string_view, size_t, uint32_t, std::vector<_RealType>&, uint32_t) [with IndexT = int; std::__cxx11::string = std::__cxx11::basic_string; nonstd::sv_lite::string_view = nonstd::sv_lite::basic_string_view; size_t = long unsigned int; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:777:41: required from 'void indexTranscriptsSA(ParserT*, std::__cxx11::string&, bool, bool, uint32_t, bool, std::__cxx11::string&, std::mutex&, std::shared_ptr) [with ParserT = fastx_parser::FastxParser; std::__cxx11::string = std::__cxx11::basic_string; uint32_t = unsigned int]' +/build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:916:102: required from here +/build/rapmap-0.12.0+dfsg/include/sparsepp/spp.h:1384:19: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess] + memcpy(_group + i, _group + i-1, sizeof(*_group)); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/utility:70, + from /usr/include/c++/8/algorithm:60, + from /build/rapmap-0.12.0+dfsg/src/RapMapSAIndexer.cpp:22: +/usr/include/c++/8/bits/stl_pair.h:208:12: note: 'spp::sparsegroup, spp::libc_allocator > >::value_type' {aka 'struct std::pair'} declared here + struct pair + ^~~~ cc1plus: warning: unrecognized command line option '-Wno-unused-local-typedef' cc1plus: warning: unrecognized command line option '-Wno-unused-local-typedef' At global scope: @@ -1131,12 +1165,12 @@ Test project /build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu Start 1: quasi_map_test Start 2: quasi_map_test_ph -1/2 Test #1: quasi_map_test ................... Passed 0.23 sec -2/2 Test #2: quasi_map_test_ph ................ Passed 0.25 sec +1/2 Test #2: quasi_map_test_ph ................ Passed 0.56 sec +2/2 Test #1: quasi_map_test ................... Passed 0.62 sec 100% tests passed, 0 tests failed out of 2 -Total Test time (real) = 0.25 sec +Total Test time (real) = 0.63 sec make[1]: Leaving directory '/build/rapmap-0.12.0+dfsg/obj-aarch64-linux-gnu' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary @@ -1189,9 +1223,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'rapmap' in '../rapmap_0.12.0+dfsg-3_arm64.deb'. dpkg-deb: building package 'rapmap-dbgsym' in '../rapmap-dbgsym_0.12.0+dfsg-3_arm64.deb'. dpkg-deb: building package 'rapmap-example-data' in '../rapmap-example-data_0.12.0+dfsg-3_all.deb'. +dpkg-deb: building package 'rapmap' in '../rapmap_0.12.0+dfsg-3_arm64.deb'. dpkg-deb: building package 'rapmap-dev' in '../rapmap-dev_0.12.0+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../rapmap_0.12.0+dfsg-3_arm64.changes @@ -1199,12 +1233,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/27180/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/27180/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/30864 and its subdirectories -I: Current time: Wed Jul 29 14:35:16 -12 2020 -I: pbuilder-time-stamp: 1596076516 +I: removing directory /srv/workspace/pbuilder/27180 and its subdirectories +I: Current time: Wed Sep 1 23:03:39 +14 2021 +I: pbuilder-time-stamp: 1630487019