I: pbuilder: network access will be disabled during build I: Current time: Thu Mar 21 04:54:39 -12 2024 I: pbuilder-time-stamp: 1711040079 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [ivar_1.3+dfsg-1.dsc] I: copying [./ivar_1.3+dfsg.orig.tar.xz] I: copying [./ivar_1.3+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.mromYDLh/trustedkeys.kbx': General error gpgv: Signature made Sun Dec 13 10:44:37 2020 -12 gpgv: using RSA key E50AFD55ADD27AAB97163A8B21D20589974B3E96 gpgv: issuer "tmancill@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./ivar_1.3+dfsg-1.dsc dpkg-source: info: extracting ivar in ivar-1.3+dfsg dpkg-source: info: unpacking ivar_1.3+dfsg.orig.tar.xz dpkg-source: info: unpacking ivar_1.3+dfsg-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/19415/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=3 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='c6ac386efa2946f89c1765570ed87d46' 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='19415' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.gRI5Elyi/pbuilderrc_wnbH --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.gRI5Elyi/b1 --logfile b1/build.log ivar_1.3+dfsg-1.dsc' SUDO_GID='112' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32b 6.1.0-18-armmp-lpae #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Mar 27 2022 bash -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 26052 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 26052 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 9636 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 26668 Sep 22 2020 cat -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash -rwxr-xr-x 1 root root 75880 Sep 22 2020 date -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd -rwxr-xr-x 1 root root 59912 Sep 22 2020 df -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir -rwxr-xr-x 1 root root 55012 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 22508 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep -rwxr-xr-x 1 root root 22496 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 47492 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 26076 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 124508 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 64212 Apr 9 2022 gzip -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln -rwxr-xr-x 1 root root 35068 Feb 7 2020 login -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls -rwxr-xr-x 1 root root 99940 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 34408 Jan 20 2022 more -rwsr-xr-x 1 root root 34400 Jan 20 2022 mount -rwxr-xr-x 1 root root 9824 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 88524 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 26652 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Mar 7 01:40 sh -> dash -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty -rwsr-xr-x 1 root root 46704 Jan 20 2022 su -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync -rwxr-xr-x 1 root root 340872 Jan 19 21:59 tar -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch -rwxr-xr-x 1 root root 22496 Sep 22 2020 true -rwxr-xr-x 1 root root 9636 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 22108 Jan 20 2022 umount -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir -rwxr-xr-x 1 root root 38512 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/19415/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libhts-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19454 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libicu67{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 47 newly installed, 0 to remove and 0 not upgraded. Need to get 24.0 MB of archives. After unpacking 73.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8+deb11u1 [139 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3+deb11u1 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3+deb11u1 [120 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3+deb11u1 [68.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7+deb11u4 [602 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf libbrotli1 armhf 1.0.9-2+b2 [262 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2.1+deb11u1 [67.7 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf libsasl2-2 armhf 2.1.27+dfsg-2.1+deb11u1 [99.2 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf libldap-2.4-2 armhf 2.4.57+dfsg-3+deb11u1 [210 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf libnghttp2-14 armhf 1.43.0-1+deb11u1 [66.7 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf libpsl5 armhf 0.21.0-1.2 [56.1 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf libssh2-1 armhf 1.9.0-2 [143 kB] Get: 40 http://deb.debian.org/debian bullseye/main armhf libcurl3-gnutls armhf 7.74.0-1.3+deb11u11 [311 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3+deb11u11 [408 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf libdeflate0 armhf 1.7-1 [43.1 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf libdeflate-dev armhf 1.7-1 [39.9 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf libhts3 armhf 1.11-4 [332 kB] Get: 45 http://deb.debian.org/debian bullseye/main armhf liblzma-dev armhf 5.2.5-2.1~deb11u1 [220 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2+deb11u2 [185 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf libhts-dev armhf 1.11-4 [3819 kB] Fetched 24.0 MB in 1s (32.0 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 ... 19454 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u1_armhf.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_armhf.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_armhf.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3+deb11u1_armhf.deb ... Unpacking libmagic-mgc (1:5.39-3+deb11u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../07-libmagic1_1%3a5.39-3+deb11u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.39-3+deb11u1) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3+deb11u1_armhf.deb ... Unpacking file (1:5.39-3+deb11u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_armhf.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../10-libsigsegv2_2.13-1_armhf.deb ... Unpacking libsigsegv2:armhf (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_armhf.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../23-libelf1_0.183-1_armhf.deb ... Unpacking libelf1:armhf (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_armhf.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:armhf. Preparing to unpack .../25-libicu67_67.1-7_armhf.deb ... Unpacking libicu67:armhf (67.1-7) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7+deb11u4_armhf.deb ... Unpacking libxml2:armhf (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_armhf.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../31-libbrotli1_1.0.9-2+b2_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../32-libsasl2-modules-db_2.1.27+dfsg-2.1+deb11u1_armhf.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/ivar-1.3+dfsg/ && 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 > ../ivar_1.3+dfsg-1_source.changes dpkg-buildpackage: info: source package ivar dpkg-buildpackage: info: source version 1.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/ivar-1.3+dfsg' rm -f data/db/test_ref.fa.fai data/test.gap.fa data/test.gap.qual.txt data/test.indel.tsv data/test.masked_primer_indices.txt data/test.trimmed.masked.bam data/test.trimmed.masked.bam.bai data/test.trimmed.sorted.bam.bai data/test.unmapped.sorted.bam.bai make[1]: Leaving directory '/build/reproducible-path/ivar-1.3+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf configure.ac:12: installing './compile' configure.ac:6: installing './install-sh' configure.ac:6: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gawk... (cached) mawk checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking for main in -lhts... no checking for main in -lpthread... no checking for main in -lz... no checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for int16_t... yes checking for int32_t... yes checking for int8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint8_t... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... no checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... no checking for memmove... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build make -j3 make[1]: Entering directory '/build/reproducible-path/ivar-1.3+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/ivar-1.3+dfsg' Making all in src make[3]: Entering directory '/build/reproducible-path/ivar-1.3+dfsg/src' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o ivar.o ivar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_consensus_pileup.o call_consensus_pileup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o alignment.o alignment.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' /usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ivar.cpp -quiet -dumpbase ivar.cpp -mfloat-abi=hard -mfpu=vfpv3-d16 -mthumb -mtls-dialect=gnu -march=armv7-a+fp -auxbase-strip ivar.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccLbkEMX.s Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' Using built-in specs. /usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 alignment.cpp -quiet -dumpbase alignment.cpp -mfloat-abi=hard -mfpu=vfpv3-d16 -mthumb -mtls-dialect=gnu -march=armv7-a+fp -auxbase-strip alignment.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/cceDKNy6.s COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' /usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_consensus_pileup.cpp -quiet -dumpbase call_consensus_pileup.cpp -mfloat-abi=hard -mfpu=vfpv3-d16 -mthumb -mtls-dialect=gnu -march=armv7-a+fp -auxbase-strip call_consensus_pileup.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccd36Tk3.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10" ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: #include "..." search starts here: . .. #include <...> search starts here: /usr/include/c++/10 . /usr/include/arm-linux-gnueabihf/c++/10 .. /usr/include/c++/10/backward /usr/include/c++/10 /usr/lib/gcc/arm-linux-gnueabihf/10/include /usr/include/arm-linux-gnueabihf/c++/10 /usr/local/include /usr/include/c++/10/backward /usr/include/arm-linux-gnueabihf /usr/lib/gcc/arm-linux-gnueabihf/10/include /usr/include /usr/local/include /usr/include/arm-linux-gnueabihf End of search list. /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/arm-linux-gnueabihf/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/arm-linux-gnueabihf/10/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: a889319284317205811f91cc96f021b9 Compiler executable checksum: a889319284317205811f91cc96f021b9 Compiler executable checksum: a889319284317205811f91cc96f021b9 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=vfpv3-d16 -meabi=5 -o alignment.o /tmp/cceDKNy6.s GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' /usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 suffix_tree.cpp -quiet -dumpbase suffix_tree.cpp -mfloat-abi=hard -mfpu=vfpv3-d16 -mthumb -mtls-dialect=gnu -march=armv7-a+fp -auxbase-strip suffix_tree.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/cc7Hht9K.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/arm-linux-gnueabihf/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/arm-linux-gnueabihf/10/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: a889319284317205811f91cc96f021b9 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=vfpv3-d16 -meabi=5 -o call_consensus_pileup.o /tmp/ccd36Tk3.s GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' /usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.cpp -mfloat-abi=hard -mfpu=vfpv3-d16 -mthumb -mtls-dialect=gnu -march=armv7-a+fp -auxbase-strip trim_primer_quality.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/cc7xcHA0.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/arm-linux-gnueabihf/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/arm-linux-gnueabihf/10/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: a889319284317205811f91cc96f021b9 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=vfpv3-d16 -meabi=5 -o suffix_tree.o /tmp/cc7Hht9K.s GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=vfpv3-d16 -meabi=5 -o ivar.o /tmp/ccLbkEMX.s GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' /usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 remove_reads_from_amplicon.cpp -quiet -dumpbase remove_reads_from_amplicon.cpp -mfloat-abi=hard -mfpu=vfpv3-d16 -mthumb -mtls-dialect=gnu -march=armv7-a+fp -auxbase-strip remove_reads_from_amplicon.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccU5aWGi.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/arm-linux-gnueabihf/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/arm-linux-gnueabihf/10/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' /usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -mfloat-abi=hard -mfpu=vfpv3-d16 -mthumb -mtls-dialect=gnu -march=armv7-a+fp -auxbase-strip call_variants.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/cclK5Igq.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/arm-linux-gnueabihf/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/arm-linux-gnueabihf/10/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: a889319284317205811f91cc96f021b9 Compiler executable checksum: a889319284317205811f91cc96f021b9 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=vfpv3-d16 -meabi=5 -o trim_primer_quality.o /tmp/cc7xcHA0.s GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' /usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 primer_bed.cpp -quiet -dumpbase primer_bed.cpp -mfloat-abi=hard -mfpu=vfpv3-d16 -mthumb -mtls-dialect=gnu -march=armv7-a+fp -auxbase-strip primer_bed.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccfJoZt7.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/arm-linux-gnueabihf/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/arm-linux-gnueabihf/10/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: a889319284317205811f91cc96f021b9 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=vfpv3-d16 -meabi=5 -o remove_reads_from_amplicon.o /tmp/ccU5aWGi.s GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' /usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 allele_functions.cpp -quiet -dumpbase allele_functions.cpp -mfloat-abi=hard -mfpu=vfpv3-d16 -mthumb -mtls-dialect=gnu -march=armv7-a+fp -auxbase-strip allele_functions.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccwEe0ZF.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/arm-linux-gnueabihf/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/arm-linux-gnueabihf/10/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: a889319284317205811f91cc96f021b9 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=vfpv3-d16 -meabi=5 -o call_variants.o /tmp/cclK5Igq.s GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' /usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_masked_amplicons.cpp -quiet -dumpbase get_masked_amplicons.cpp -mfloat-abi=hard -mfpu=vfpv3-d16 -mthumb -mtls-dialect=gnu -march=armv7-a+fp -auxbase-strip get_masked_amplicons.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccMNLLMD.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/arm-linux-gnueabihf/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/arm-linux-gnueabihf/10/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: a889319284317205811f91cc96f021b9 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=vfpv3-d16 -meabi=5 -o primer_bed.o /tmp/ccfJoZt7.s GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' /usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_common_variants.cpp -quiet -dumpbase get_common_variants.cpp -mfloat-abi=hard -mfpu=vfpv3-d16 -mthumb -mtls-dialect=gnu -march=armv7-a+fp -auxbase-strip get_common_variants.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccaYc2GI.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/arm-linux-gnueabihf/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/arm-linux-gnueabihf/10/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: a889319284317205811f91cc96f021b9 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=vfpv3-d16 -meabi=5 -o allele_functions.o /tmp/ccwEe0ZF.s GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' /usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 parse_gff.cpp -quiet -dumpbase parse_gff.cpp -mfloat-abi=hard -mfpu=vfpv3-d16 -mthumb -mtls-dialect=gnu -march=armv7-a+fp -auxbase-strip parse_gff.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccaMGOdB.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/arm-linux-gnueabihf/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/arm-linux-gnueabihf/10/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: a889319284317205811f91cc96f021b9 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=vfpv3-d16 -meabi=5 -o get_masked_amplicons.o /tmp/ccMNLLMD.s GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' /usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ref_seq.cpp -quiet -dumpbase ref_seq.cpp -mfloat-abi=hard -mfpu=vfpv3-d16 -mthumb -mtls-dialect=gnu -march=armv7-a+fp -auxbase-strip ref_seq.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccOrGaJT.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/arm-linux-gnueabihf/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/arm-linux-gnueabihf/10/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: a889319284317205811f91cc96f021b9 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=vfpv3-d16 -meabi=5 -o get_common_variants.o /tmp/ccaYc2GI.s GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp Using built-in specs. COLLECT_GCC=g++ Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' /usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -mfloat-abi=hard -mfpu=vfpv3-d16 -mthumb -mtls-dialect=gnu -march=armv7-a+fp -auxbase-strip interval_tree.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccuxhN5M.s GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10" ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed" ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include" #include "..." search starts here: #include <...> search starts here: . .. /usr/include/c++/10 /usr/include/arm-linux-gnueabihf/c++/10 /usr/include/c++/10/backward /usr/lib/gcc/arm-linux-gnueabihf/10/include /usr/local/include /usr/include/arm-linux-gnueabihf /usr/include End of search list. GNU C++11 (Debian 10.2.1-6) version 10.2.1 20210110 (arm-linux-gnueabihf) compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: a889319284317205811f91cc96f021b9 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=vfpv3-d16 -meabi=5 -o interval_tree.o /tmp/ccuxhN5M.s GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=vfpv3-d16 -meabi=5 -o ref_seq.o /tmp/ccOrGaJT.s GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' In file included from /usr/include/c++/10/vector:67, from /usr/include/c++/10/regex:51, from parse_gff.h:4, from parse_gff.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In copy constructor ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/stl_vector.h:558:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 558 | std::__uninitialized_copy_a(__x.begin(), __x.end(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 559 | this->_M_impl._M_start, | ~~~~~~~~~~~~~~~~~~~~~~~ 560 | _M_get_Tp_allocator()); | ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:66, from /usr/include/c++/10/regex:45, from parse_gff.h:4, from parse_gff.cpp:1: /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’: /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 325 | { return std::uninitialized_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/regex:51, from parse_gff.h:4, from parse_gff.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:66, from /usr/include/c++/10/regex:45, from parse_gff.h:4, from parse_gff.cpp:1: /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gff3_feature*]’: /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 125 | uninitialized_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 147 | return std::__uninitialized_copy<__is_trivial(_ValueType1) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 148 | && __is_trivial(_ValueType2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | && __assignable>:: | ~~~~~~~~~~~~~~~~~~ 150 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/regex:51, from parse_gff.h:4, from parse_gff.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:66, from /usr/include/c++/10/regex:45, from parse_gff.h:4, from parse_gff.cpp:1: /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gff3_feature*; _ForwardIterator = gff3_feature*; _Allocator = std::allocator]’: /usr/include/c++/10/bits/stl_uninitialized.h:347:2: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 346 | return std::__uninitialized_copy_a | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 347 | (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 348 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’: /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 84 | __uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’: /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 325 | { return std::uninitialized_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gff3_feature*]’: /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 125 | uninitialized_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 147 | return std::__uninitialized_copy<__is_trivial(_ValueType1) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 148 | && __is_trivial(_ValueType2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | && __assignable>:: | ~~~~~~~~~~~~~~~~~~ 150 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’: /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 84 | __uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' as -v -I . -I .. -march=armv7-a -mfloat-abi=hard -mfpu=vfpv3-d16 -meabi=5 -o parse_gff.o /tmp/ccaMGOdB.s GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Debian) 2.35.2 MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' g++ -v -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o ivar ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper Target: arm-linux-gnueabihf Configured with: ../src/configure -v --with-pkgversion='Debian 10.2.1-6' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv7-a --with-fpu=vfpv3-d16 --with-float=hard --with-mode=thumb --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 10.2.1 20210110 (Debian 10.2.1-6) MAKEFLAGS=w -j3 COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/ LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/ COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' /usr/lib/gcc/arm-linux-gnueabihf/10/collect2 -plugin /usr/lib/gcc/arm-linux-gnueabihf/10/liblto_plugin.so -plugin-opt=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper -plugin-opt=-fresolution=/tmp/cc8TGDJb.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -dynamic-linker /lib/ld-linux-armhf.so.3 -X --hash-style=gnu --as-needed -m armelf_linux_eabi -pie -o ivar /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/Scrt1.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/crtbeginS.o -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crtn.o COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfpv3-d16' '-mthumb' '-mtls-dialect=gnu' '-march=armv7-a+fp' make[3]: Leaving directory '/build/reproducible-path/ivar-1.3+dfsg/src' Making all in tests make[3]: Entering directory '/build/reproducible-path/ivar-1.3+dfsg/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/ivar-1.3+dfsg/tests' make[3]: Entering directory '/build/reproducible-path/ivar-1.3+dfsg' make[3]: Leaving directory '/build/reproducible-path/ivar-1.3+dfsg' make[2]: Leaving directory '/build/reproducible-path/ivar-1.3+dfsg' make[1]: Leaving directory '/build/reproducible-path/ivar-1.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/ivar-1.3+dfsg' dh_auto_test --no-parallel make -j1 check VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/ivar-1.3+dfsg' Making check in src make[3]: Entering directory '/build/reproducible-path/ivar-1.3+dfsg/src' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/reproducible-path/ivar-1.3+dfsg/src' Making check in tests make[3]: Entering directory '/build/reproducible-path/ivar-1.3+dfsg/tests' make check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search make[4]: Entering directory '/build/reproducible-path/ivar-1.3+dfsg/tests' g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_trim.o test_primer_trim.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/trim_primer_quality.o ../src/trim_primer_quality.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/primer_bed.o ../src/primer_bed.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/interval_tree.o ../src/interval_tree.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_trim test_primer_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_trim.o test_trim.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_trim test_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o check_quality_trim.o check_quality_trim.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_quality_trim check_quality_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_call_consensus_from_plup.o test_call_consensus_from_plup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/call_consensus_pileup.o ../src/call_consensus_pileup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/allele_functions.o ../src/allele_functions.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus test_call_consensus_from_plup.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_allele_depth.o test_allele_depth.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_allele_depth test_allele_depth.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_threshold.o test_consensus_threshold.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_threshold test_consensus_threshold.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_min_depth.o test_consensus_min_depth.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_min_depth test_consensus_min_depth.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_seq_id.o test_consensus_seq_id.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_seq_id test_consensus_seq_id.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_bed.o test_primer_bed.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_bed test_primer_bed.o ../src/primer_bed.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_getmasked.o test_getmasked.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/get_masked_amplicons.o ../src/get_masked_amplicons.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_getmasked test_getmasked.o ../src/get_masked_amplicons.o ../src/primer_bed.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_removereads.o test_removereads.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/remove_reads_from_amplicon.o ../src/remove_reads_from_amplicon.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_removereads test_removereads.o ../src/remove_reads_from_amplicon.o ../src/primer_bed.o ../src/trim_primer_quality.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_variants.o test_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/call_variants.o ../src/call_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/parse_gff.o ../src/parse_gff.cpp In file included from /usr/include/c++/10/vector:67, from /usr/include/c++/10/regex:51, from ../src/parse_gff.h:4, from ../src/parse_gff.cpp:1: /usr/include/c++/10/bits/stl_vector.h: In copy constructor ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/stl_vector.h:558:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 558 | std::__uninitialized_copy_a(__x.begin(), __x.end(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 559 | this->_M_impl._M_start, | ~~~~~~~~~~~~~~~~~~~~~~~ 560 | _M_get_Tp_allocator()); | ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:66, from /usr/include/c++/10/regex:45, from ../src/parse_gff.h:4, from ../src/parse_gff.cpp:1: /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’: /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 325 | { return std::uninitialized_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/regex:51, from ../src/parse_gff.h:4, from ../src/parse_gff.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:66, from /usr/include/c++/10/regex:45, from ../src/parse_gff.h:4, from ../src/parse_gff.cpp:1: /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gff3_feature*]’: /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 125 | uninitialized_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 147 | return std::__uninitialized_copy<__is_trivial(_ValueType1) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 148 | && __is_trivial(_ValueType2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | && __assignable>:: | ~~~~~~~~~~~~~~~~~~ 150 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/vector:72, from /usr/include/c++/10/regex:51, from ../src/parse_gff.h:4, from ../src/parse_gff.cpp:1: /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator]’: /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/10/memory:66, from /usr/include/c++/10/regex:45, from ../src/parse_gff.h:4, from ../src/parse_gff.cpp:1: /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gff3_feature*; _ForwardIterator = gff3_feature*; _Allocator = std::allocator]’: /usr/include/c++/10/bits/stl_uninitialized.h:347:2: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 346 | return std::__uninitialized_copy_a | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 347 | (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 348 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’: /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 84 | __uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’: /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 325 | { return std::uninitialized_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gff3_feature*]’: /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 125 | uninitialized_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 /usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 147 | return std::__uninitialized_copy<__is_trivial(_ValueType1) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 148 | && __is_trivial(_ValueType2) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 | && __assignable>:: | ~~~~~~~~~~~~~~~~~~ 150 | __uninit_copy(__first, __last, __result); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’: /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 84 | __uninit_copy(_InputIterator __first, _InputIterator __last, | ^~~~~~~~~~~~~ /usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘std::move_iterator’ changed in GCC 7.1 g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/ref_seq.o ../src/ref_seq.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_variants test_variants.o ../src/call_variants.o ../src/allele_functions.o ../src/parse_gff.o ../src/ref_seq.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_common_variants.o test_common_variants.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/get_common_variants.o ../src/get_common_variants.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_common_variants test_common_variants.o ../src/get_common_variants.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_unpaired_trim.o test_unpaired_trim.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_unpaired_trim test_unpaired_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_trim_edge_cases.o test_primer_trim_edge_cases.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_trim_edge_cases test_primer_trim_edge_cases.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_isize_trim.o test_isize_trim.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_isize_trim test_isize_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_interval_tree.o test_interval_tree.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_interval_tree test_interval_tree.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o test_amplicon_search.o test_amplicon_search.cpp g++ -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_amplicon_search test_amplicon_search.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread make[4]: Leaving directory '/build/reproducible-path/ivar-1.3+dfsg/tests' make check-TESTS make[4]: Entering directory '/build/reproducible-path/ivar-1.3+dfsg/tests' make[5]: Entering directory '/build/reproducible-path/ivar-1.3+dfsg/tests' FAIL: check_primer_trim PASS: check_trim PASS: check_quality_trim PASS: check_consensus PASS: check_allele_depth PASS: check_consensus_threshold PASS: check_consensus_min_depth PASS: check_consensus_seq_id PASS: check_primer_bed PASS: check_getmasked PASS: check_removereads PASS: check_variants PASS: check_common_variants FAIL: check_unpaired_trim PASS: check_primer_trim_edge_cases PASS: check_isize_trim PASS: check_interval_tree PASS: check_amplicon_search ==================================== ivar 1.3: tests/test-suite.log ==================================== # TOTAL: 18 # PASS: 16 # SKIP: 0 # XFAIL: 0 # FAIL: 2 # XPASS: 0 # ERROR: 0 .. contents:: :depth: 2 FAIL: check_primer_trim ======================= Found 8 primers in BED file [E::idx_find_and_load] Could not retrieve index file for '../data/test.unmapped.sorted.bam' test_outside_primer ---- test_20_381_1:0:0_6:0:0_1_150 0-6 6-1 0-5 1-1 0-139 Condensing cigar ... 4-12 0-139 ---- test_20_381_1_softclip:0:0_6:0:0_1_150 4-24 0-3 2-2 0-1 1-1 0-4 2-1 6-1 2-1 0-114 Condensing cigar ... 4-33 0-114 ---- test_67_308_2:0:0_2:0:0_0_100 ---- test_67_308_2:0:0_2:0:0_0_100 ---- test_200_349_0:0:0_6:0:0_2_25 ---- test_200_349_0:0:0_6:0:0_2_25 ---- test_20_381_1:0:0_6:0:0_1_150 0-121 6-1 2-4 0-4 2-1 0-1 6-1 0-1 2-1 0-11 4-6 Condensing cigar ... 0-121 4-23 ---- test_20_381_1_softclip:0:0_6:0:0_1_150 0-103 1-1 0-10 1-1 0-13 4-24 Condensing cigar ... 0-103 4-49 ---- test_outside_primer 0-41 2-3 0-57 6-1 0-10 6-1 0-39 Incorrect start position Cigar flag didn't match for 6 ! Expected 2 Got 0 Cigar length didn't match for test_outside_primer ! Expected 3 Got 57 Cigar flag didn't match for 6 ! Expected 0 Got 6 Cigar length didn't match for test_outside_primer ! Expected 57 Got 1 Cigar flag didn't match for 6 ! Expected 6 Got 0 Cigar length didn't match for test_outside_primer ! Expected 1 Got 10 Cigar flag didn't match for 6 ! Expected 0 Got 6 Cigar length didn't match for test_outside_primer ! Expected 10 Got 1 Cigar flag didn't match for 6 ! Expected 6 Got 0 Cigar length didn't match for test_outside_primer ! Expected 1 Got 39 Condensing cigar ... 4-23 0-75 6-1 0-10 6-1 0-39 Cigar length didn't match after condense! Expected 18 Got 75 Cigar flag didn't match! Expected  Got 6 Cigar length didn't match after condense! Expected 3 Got 1 Cigar length didn't match after condense! Expected 57 Got 10 Cigar length didn't match after condense! Expected 10 Got 39 ---- FAIL check_primer_trim (exit status: 255) FAIL: check_unpaired_trim ========================= Found 8 primers in BED file test_72_280_12:1:0_11:0:0_2 Forward Reverse Cigar flag didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 2 Got 0 Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 2 Got 1 Cigar flag didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 0 Got 4 Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 1 Got 3 Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 3 Got 2 Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 2 Got 8 Condensing cigar ... Cigar length didn't match after condense! Expected 93 Got 94 Cigar flag didn't match! Expected  Got 4 Cigar length didn't match after condense! Expected 2 Got 13 test_92_337_8:0:0_10:0:0_21 Forward Reverse Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 1 Got 56 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 56 Got 1 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 1 Got 6 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 3 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 3 Got 99 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 99 Got 2 Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0 Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 2 Got 65 Condensing cigar ... Cigar length didn't match after condense! Expected 19 Got 75 Cigar length didn't match after condense! Expected 56 Got 6 Cigar length didn't match after condense! Expected 1 Got 3 Cigar length didn't match after condense! Expected 6 Got 99 Cigar length didn't match after condense! Expected 3 Got 2 Cigar length didn't match after condense! Expected 99 Got 65 test_147_337_11:1:0_11:1:0_11 Forward Reverse Condensing cigar ... test_149_298_7:0:0_11:0:0_d Forward Reverse Condensing cigar ... test_184_379_11:1:0_8:1:0_26 Forward Reverse Cigar flag didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 6 Got 0 Cigar length didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 2 Got 89 Cigar flag didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 0 Got 4 Cigar length didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 89 Got 18 Condensing cigar ... Cigar length didn't match after condense! Expected 71 Got 160 Cigar flag didn't match! Expected  Got 4 Cigar length didn't match after condense! Expected 2 Got 18 FAIL check_unpaired_trim (exit status: 255) ============================================================================ Testsuite summary for ivar 1.3 ============================================================================ # TOTAL: 18 # PASS: 16 # SKIP: 0 # XFAIL: 0 # FAIL: 2 # XPASS: 0 # ERROR: 0 ============================================================================ See tests/test-suite.log Please report to gkarthik@scripps.edu ============================================================================ make[5]: *** [Makefile:904: test-suite.log] Error 1 make[5]: Leaving directory '/build/reproducible-path/ivar-1.3+dfsg/tests' make[4]: *** [Makefile:1012: check-TESTS] Error 2 make[4]: Leaving directory '/build/reproducible-path/ivar-1.3+dfsg/tests' make[3]: *** [Makefile:1205: check-am] Error 2 make[3]: Leaving directory '/build/reproducible-path/ivar-1.3+dfsg/tests' make[2]: *** [Makefile:362: check-recursive] Error 1 make[2]: Leaving directory '/build/reproducible-path/ivar-1.3+dfsg' dh_auto_test: error: make -j1 check VERBOSE=1 returned exit code 2 make[1]: *** [debian/rules:12: override_dh_auto_test] Error 25 make[1]: Leaving directory '/build/reproducible-path/ivar-1.3+dfsg' make: *** [debian/rules:9: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/19415 and its subdirectories