Sun Jul 28 11:07:06 UTC 2024 I: starting to build jellyfish1/bullseye/amd64 on jenkins on '2024-07-28 11:06' Sun Jul 28 11:07:06 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_5/14781/console.log Sun Jul 28 11:07:06 UTC 2024 I: Downloading source for bullseye/jellyfish1=1.1.11-5 --2024-07-28 11:07:06-- http://cdn-fastly.deb.debian.org/debian/pool/main/j/jellyfish1/jellyfish1_1.1.11-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2015 (2.0K) [text/prs.lines.tag] Saving to: ‘jellyfish1_1.1.11-5.dsc’ 0K . 100% 230M=0s 2024-07-28 11:07:06 (230 MB/s) - ‘jellyfish1_1.1.11-5.dsc’ saved [2015/2015] Sun Jul 28 11:07:06 UTC 2024 I: jellyfish1_1.1.11-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: jellyfish1 Binary: jellyfish1 Architecture: any Version: 1.1.11-5 Maintainer: Debian Med Packaging Team Uploaders: Shaun Jackman , Andreas Tille Homepage: https://www.cbcb.umd.edu/software/jellyfish/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/jellyfish1 Vcs-Git: https://salsa.debian.org/med-team/jellyfish1.git Build-Depends: debhelper-compat (= 13) Package-List: jellyfish1 deb science optional arch=any Checksums-Sha1: 8bd6a7b382e94d37adfddd916dec2b0e36f840fd 1067138 jellyfish1_1.1.11.orig.tar.gz a0d7aa2ce53dfef055a55bbedcc302ea166460e7 5016 jellyfish1_1.1.11-5.debian.tar.xz Checksums-Sha256: 496645d96b08ba35db1f856d857a159798c73cbc1eccb852ef1b253d1678c8e2 1067138 jellyfish1_1.1.11.orig.tar.gz 37eae87742011610c68078ac1fda923bedcba924fca4161969493f8ca84819da 5016 jellyfish1_1.1.11-5.debian.tar.xz Files: dc994ea8b0896156500ea8c648f24846 1067138 jellyfish1_1.1.11.orig.tar.gz d49be598ea2ed67eedb246e5db1878cb 5016 jellyfish1_1.1.11-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+/VbkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGMPg//RYlbAb0zUJI+Ww/w5Od9wEWqyMUDt7IA mwKdB1NHB3zFtkBD6Ayg5pezNzFXfR8dNvwUy347Ch/k2md9DgRtugxgRbcT4139 K6X+vZ0bNXyKIE/E+O2pp6rmneYH3cpirRK7K6JyJW2wyy4et9m5Iow5z+SXHUU7 uXNbpJmlOHyhKSHibUV1Nm/SuMXQ6CL0MqDRAC9NeaA5UOsVpualV+tHudWzIzMm tcOe+tQnKcjBXPLXhHel3UywDOtTpLQ7BtKK7+mP6KNrVZq1yPDByNXHVgdEUx5q Ocs19QKzyclyL45mXgy3xxZij7jyeAdPRfuUwaSt/XvMzxgPPMlyqYYzCMv+jkeV mHZjfUyXTLBmamw2PdLzn73G70JUuyyvWGH02tdd63DcmVpQT8J/UXjQziNoGsuA QmL7ZHsutO791XGATknPmR/DbvoXdX4oA5YS3z0ciwqyXbfrBxTTvxcOLgOIYzDV QfY2vW63Nxe/mVJnkHZZqv+QyXEjR4bHkaAsoDdzZlVyTHIhQjlPlPYDunuY2KOs 1SZGaKWtZ/FjIzGwLuo1HFG/1dL7LiyX+ZxpmPs4ADVNhqtmo6AiwnqSeo6Z/dN1 ADFmsdgKGhrQYEjAXLtAMS0pKidfmkF8t9CGy2PkQfpCBs1zVr53563xwUFqR71b lr7EuThz42k= =rg+M -----END PGP SIGNATURE----- Sun Jul 28 11:07:07 UTC 2024 I: Checking whether the package is not for us Sun Jul 28 11:07:07 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Sun Jul 28 11:07:07 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Sun Jul 28 11:10:04 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Jul 27 23:07:09 -12 2024 I: pbuilder-time-stamp: 1722164829 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 [jellyfish1_1.1.11-5.dsc] I: copying [./jellyfish1_1.1.11.orig.tar.gz] I: copying [./jellyfish1_1.1.11-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.iwzl55Ly/trustedkeys.kbx': General error gpgv: Signature made Wed Nov 25 19:14:01 2020 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./jellyfish1_1.1.11-5.dsc dpkg-source: info: extracting jellyfish1 in jellyfish1-1.1.11 dpkg-source: info: unpacking jellyfish1_1.1.11.orig.tar.gz dpkg-source: info: unpacking jellyfish1_1.1.11-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying man dpkg-source: info: applying arm64.patch dpkg-source: info: applying mips.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3667473/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=20 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='0479d40f3a4148d18e7a695e52b5389f' 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='3667473' 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.ZhBxk5K5/pbuilderrc_X1oc --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.ZhBxk5K5/b1 --logfile b1/build.log jellyfish1_1.1.11-5.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-23-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.99-1 (2024-07-15) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 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 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 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 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Mar 27 22:09 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 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Jan 24 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 69032 Mar 27 22:09 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 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 98048 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Mar 27 22:09 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Mar 27 22:09 more -rwsr-xr-x 1 root root 55528 Mar 27 22:09 mount -rwxr-xr-x 1 root root 18664 Mar 27 22:09 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 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 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 6 21:26 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Mar 27 22:09 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Jan 19 2024 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Mar 27 22:09 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Mar 27 22:09 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/3667473/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19711 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. 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} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 18.3 MB of archives. After unpacking 67.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u2 [146 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3+deb11u1 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3+deb11u1 [128 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3+deb11u1 [69.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Fetched 18.3 MB in 1s (12.9 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 ... 19711 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u2_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.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_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3+deb11u1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../07-libmagic1_1%3a5.39-3+deb11u1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3+deb11u1) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3+deb11u1_amd64.deb ... Unpacking file (1:5.39-3+deb11u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../10-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_amd64.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:amd64. Preparing to unpack .../23-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../25-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7+deb11u4_amd64.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/jellyfish1-1.1.11/ && 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 > ../jellyfish1_1.1.11-5_source.changes dpkg-buildpackage: info: source package jellyfish1 dpkg-buildpackage: info: source version 1.1.11-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/jellyfish1-1.1.11' dh_clean if [ -d debian/tmp_save_tests ] ; then \ mv debian/tmp_save_tests/* tests ; \ rmdir debian/tmp_save_tests ; \ fi make[1]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:9: installing './compile' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/jellyfish1-1.1.11' dh_auto_configure ./configure --build=x86_64-linux-gnu --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/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu 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 whether make supports nested variables... (cached) yes checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc 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 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 for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes 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 dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for md5sum... md5sum checking for __int128... yes checking whether strerror_r is declared... yes checking for strerror_r... yes checking whether strerror_r returns char *... yes checking execinfo.h usability... yes checking execinfo.h presence... yes checking for execinfo.h... yes checking sys/syscall.h usability... yes checking sys/syscall.h presence... yes checking for sys/syscall.h... yes checking for siginfo_t.si_int... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating tests/compat.sh config.status: creating jellyfish-1.1.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands make[1]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/jellyfish1-1.1.11' mkdir -p debian/tmp_save_tests cp -a tests/* debian/tmp_save_tests dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all make -j1 all bin/generate_sequence bin/test_all make[2]: Entering directory '/build/reproducible-path/jellyfish1-1.1.11' make all-am make[3]: Entering directory '/build/reproducible-path/jellyfish1-1.1.11' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/jellyfish.o jellyfish/jellyfish.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/stats_main.o jellyfish/stats_main.cc In file included from jellyfish/stats_main.cc:24: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]': ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]': ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]': ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]': ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]': ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]': ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]': ./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array::resize() [with T = char]' ./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]' ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]': ./jellyfish/raw_dumper.hpp:169:11: required from 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array]' ./jellyfish/raw_dumper.hpp:98:20: required from 'jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]' jellyfish/stats_main.cc:83:34: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/stats_main.cc:26: ./jellyfish/square_binary_matrix.hpp: In static member function 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]': ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/stats_main.cc:25: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/stats_main.cc:26: ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/stats_main.cc:25: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/hash_merge.o jellyfish/hash_merge.cc In file included from jellyfish/hash_merge.cc:32: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]': ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]': ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]': ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]': ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]': ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]': ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' In file included from ./jellyfish/mer_counting.hpp:31, from jellyfish/hash_merge.cc:34: ./jellyfish/compacted_hash.hpp: In instantiation of 'void jellyfish::compacted_hash::writer::write_header(std::ostream*) const [with storage_t = jellyfish::compacted_hash::reader; std::ostream = std::basic_ostream]': jellyfish/hash_merge.cc:189:43: required from here ./jellyfish/compacted_hash.hpp:114:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct jellyfish::compacted_hash::header'; use assignment or value-initialization instead [-Wclass-memaccess] 114 | memset(&head, '\0', sizeof(head)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/compacted_hash.hpp:36:12: note: 'struct jellyfish::compacted_hash::header' declared here 36 | struct header { | ^~~~~~ In file included from jellyfish/hash_merge.cc:32: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]': ./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array::resize() [with T = char]' ./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]' ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_merge.cc:34: ./jellyfish/square_binary_matrix.hpp: In function 'int merge_main(int, char**)': ./jellyfish/square_binary_matrix.hpp:87:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | free(columns); | ~~~~^~~~~~~~~ In file included from jellyfish/hash_merge.cc:33: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_merge.cc:34: ./jellyfish/square_binary_matrix.hpp:87:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | free(columns); | ~~~~^~~~~~~~~ In file included from jellyfish/hash_merge.cc:33: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_merge.cc:34: ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/hash_merge.cc:33: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_merge.cc:34: ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/hash_merge.cc:33: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mer_counter.o jellyfish/mer_counter.cc In file included from jellyfish/mer_counter.cc:33: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]': ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]': ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]': ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]': ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]': ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]': ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::invertible_hash::ErrorAllocation]': ./jellyfish/invertible_hash_array.hpp:116:11: required from 'jellyfish::invertible_hash::array::array(size_t, uint_t, uint_t, uint_t, size_t*) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap; size_t = long unsigned int; uint_t = long unsigned int]' jellyfish/mer_counter.cc:142:66: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::invertible_hash::InvalidMatrix]': ./jellyfish/invertible_hash_array.hpp:185:11: required from 'void jellyfish::invertible_hash::array::set_matrix(SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' jellyfish/mer_counter.cc:149:24: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]': ./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array::resize() [with T = char]' ./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]' ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::double_fifo_input::Error]': ./jellyfish/double_fifo_input.hpp:101:7: required from 'jellyfish::double_fifo_input::double_fifo_input(long unsigned int) [with T = jellyfish::sequence_parser::sequence_t]' ./jellyfish/parse_dna.hpp:178:75: required from 'jellyfish::parse_dna::parse_dna(T, T, uint_t, unsigned int, size_t) [with T = __gnu_cxx::__normal_iterator >; uint_t = long unsigned int; size_t = long unsigned int]' jellyfish/mer_counter.cc:138:60: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' In file included from ./jellyfish/mer_counting.hpp:31, from jellyfish/mer_counter.cc:38: ./jellyfish/compacted_hash.hpp: In instantiation of 'void jellyfish::compacted_hash::writer::write_header(std::ostream*) const [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; std::ostream = std::basic_ostream]': ./jellyfish/direct_sorted_dumper.hpp:101:39: required from 'void jellyfish::direct_sorted_dumper::_dump() [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; atomic_t = atomic::gcc]' ./jellyfish/direct_sorted_dumper.hpp:91:8: required from here ./jellyfish/compacted_hash.hpp:114:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct jellyfish::compacted_hash::header'; use assignment or value-initialization instead [-Wclass-memaccess] 114 | memset(&head, '\0', sizeof(head)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/compacted_hash.hpp:36:12: note: 'struct jellyfish::compacted_hash::header' declared here 36 | struct header { | ^~~~~~ ./jellyfish/compacted_hash.hpp: In instantiation of 'void jellyfish::compacted_hash::writer::write_header(std::ostream*) const [with storage_t = jellyfish::invertible_hash::array; std::ostream = std::basic_ostream]': ./jellyfish/sorted_dumper.hpp:116:39: required from 'void jellyfish::sorted_dumper::_dump() [with storage_t = jellyfish::invertible_hash::array; atomic_t = atomic::gcc]' ./jellyfish/sorted_dumper.hpp:105:8: required from here ./jellyfish/compacted_hash.hpp:114:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct jellyfish::compacted_hash::header'; use assignment or value-initialization instead [-Wclass-memaccess] 114 | memset(&head, '\0', sizeof(head)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/compacted_hash.hpp:36:12: note: 'struct jellyfish::compacted_hash::header' declared here 36 | struct header { | ^~~~~~ In file included from jellyfish/mer_counter.cc:33: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::hash, atomic::gcc>::TableFull]': ./jellyfish/hash.hpp:151:9: required from 'void jellyfish::hash::dump() [with key_t = long unsigned int; val_t = jellyfish::Float; ary_t = jellyfish::aligned_values::array; atomic = atomic::gcc]' jellyfish/mer_counter.cc:114:17: required from 'void mer_counting::start(int) [with parser_t = jellyfish::parse_quake; hash_t = jellyfish::hash, atomic::gcc>]' jellyfish/mer_counter.cc:97:8: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::hash, jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>, atomic::gcc>::TableFull]': ./jellyfish/hash.hpp:151:9: required from 'void jellyfish::hash::dump() [with key_t = long unsigned int; val_t = jellyfish::capped_integer; ary_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; atomic = atomic::gcc]' jellyfish/mer_counter.cc:114:17: required from 'void mer_counting::start(int) [with parser_t = jellyfish::parse_qual_dna; hash_t = jellyfish::hash, jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>, atomic::gcc>]' jellyfish/mer_counter.cc:97:8: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::hash, atomic::gcc>::TableFull]': ./jellyfish/hash.hpp:151:9: required from 'void jellyfish::hash::dump() [with key_t = long unsigned int; val_t = long unsigned int; ary_t = jellyfish::invertible_hash::array; atomic = atomic::gcc]' jellyfish/mer_counter.cc:114:17: required from 'void mer_counting::start(int) [with parser_t = jellyfish::parse_qual_dna; hash_t = jellyfish::hash, atomic::gcc>]' jellyfish/mer_counter.cc:97:8: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' In file included from jellyfish/mer_counter.cc:36: ./jellyfish/misc.hpp: In member function 'void jellyfish::direct_sorted_dumper::_dump() [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; atomic_t = atomic::gcc]': ./jellyfish/misc.hpp:106:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/mer_counter.cc:38: ./jellyfish/square_binary_matrix.hpp: In member function 'void jellyfish::invertible_hash::array::set_matrix(SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]': ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/mer_counter.cc:36: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/histo_main.o jellyfish/histo_main.cc In file included from jellyfish/histo_main.cc:25: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]': ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]': ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]': ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]': ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]': ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]': ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]': ./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array::resize() [with T = char]' ./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]' ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]': ./jellyfish/raw_dumper.hpp:169:11: required from 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array]' ./jellyfish/raw_dumper.hpp:98:20: required from 'jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]' jellyfish/histo_main.cc:111:34: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_main.cc:27: ./jellyfish/square_binary_matrix.hpp: In static member function 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]': ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/histo_main.cc:26: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_main.cc:27: ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/histo_main.cc:26: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_main.cc:27: ./jellyfish/square_binary_matrix.hpp: In function 'int histo_main(int, char**)': ./jellyfish/square_binary_matrix.hpp:87:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | free(columns); | ~~~~^~~~~~~~~ In file included from jellyfish/histo_main.cc:26: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_main.cc:27: ./jellyfish/square_binary_matrix.hpp:87:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | free(columns); | ~~~~^~~~~~~~~ In file included from jellyfish/histo_main.cc:26: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dump_main.o jellyfish/dump_main.cc jellyfish/dump_main.cc: In function 'int dump_main(int, char**)': jellyfish/dump_main.cc:86:24: warning: catching polymorphic type 'class mapped_file::ErrorMMap' by value [-Wcatch-value=] 86 | } catch(mapped_file::ErrorMMap) { | ^~~~~~~~~ In file included from jellyfish/dump_main.cc:24: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]': ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]': ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]': ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]': ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]': ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]': ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]': ./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array::resize() [with T = char]' ./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]' ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]': ./jellyfish/raw_dumper.hpp:169:11: required from 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array]' ./jellyfish/raw_dumper.hpp:98:20: required from 'jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]' jellyfish/dump_main.cc:65:44: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/dump_main.cc:26: ./jellyfish/square_binary_matrix.hpp: In static member function 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]': ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/dump_main.cc:25: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/dump_main.cc:26: ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/dump_main.cc:25: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/query_main.o jellyfish/query_main.cc In file included from ./jellyfish/mapped_file.hpp:29, from ./jellyfish/hash.hpp:27, from ./jellyfish/mer_counting.hpp:28, from jellyfish/query_main.cc:24: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]': ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]': ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]': ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]': ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]': ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]': ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]': ./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array::resize() [with T = char]' ./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]' ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::raw_hash::ErrorReading]': ./jellyfish/raw_dumper.hpp:169:11: required from 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array]' ./jellyfish/raw_dumper.hpp:98:20: required from 'jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array]' jellyfish/query_main.cc:63:34: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/query_main.cc:24: ./jellyfish/square_binary_matrix.hpp: In static member function 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array]': ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/query_main.cc:23: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/query_main.cc:24: ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/query_main.cc:23: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dump_fastq_main.o jellyfish/dump_fastq_main.cc In file included from jellyfish/dump_fastq_main.cc:25: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]': ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]': ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]': ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]': ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]': ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]': ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]': ./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array::resize() [with T = char]' ./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]' ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/dump_fastq_main.cc:27: ./jellyfish/square_binary_matrix.hpp: In static member function 'static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]': ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/dump_fastq_main.cc:26: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/dump_fastq_main.cc:27: ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/dump_fastq_main.cc:26: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/histo_fastq_main.o jellyfish/histo_fastq_main.cc In file included from jellyfish/histo_fastq_main.cc:26: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]': ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]': ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]': ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]': ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]': ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]': ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]': ./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array::resize() [with T = char]' ./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]' ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_fastq_main.cc:28: ./jellyfish/square_binary_matrix.hpp: In static member function 'static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]': ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/histo_fastq_main.cc:27: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/histo_fastq_main.cc:28: ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/histo_fastq_main.cc:27: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/cite.o jellyfish/cite.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/hash_fastq_merge.o jellyfish/hash_fastq_merge.cc In file included from jellyfish/hash_fastq_merge.cc:17: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]': ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]': ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]': ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]': ./jellyfish/dumper.hpp:44:9: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]': ./jellyfish/compacted_hash.hpp:50:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]': ./jellyfish/fastq_dumper.hpp:46:11: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::hash, atomic::gcc>::TableFull]': ./jellyfish/hash.hpp:151:9: required from 'void jellyfish::hash::dump() [with key_t = long unsigned int; val_t = jellyfish::Float; ary_t = jellyfish::aligned_values::array; atomic = atomic::gcc]' jellyfish/hash_fastq_merge.cc:49:13: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]': ./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array::resize() [with T = char]' ./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]' ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::invertible_hash::ErrorAllocation]': ./jellyfish/invertible_hash_array.hpp:116:11: required from 'jellyfish::invertible_hash::array::array(size_t, uint_t, uint_t, uint_t, size_t*) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap; size_t = long unsigned int; uint_t = long unsigned int]' ./jellyfish/aligned_values_array.hpp:42:30: required from 'jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(size_t, uint_t, uint_t, size_t*) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap; size_t = long unsigned int; uint_t = long unsigned int]' jellyfish/hash_fastq_merge.cc:28:79: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_fastq_merge.cc:19: ./jellyfish/square_binary_matrix.hpp: In static member function 'static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]': ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/hash_fastq_merge.cc:18: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ In file included from ./jellyfish/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28, from jellyfish/hash_fastq_merge.cc:19: ./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 69 | columns[i] = rhs.columns[i] & _mask; | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from jellyfish/hash_fastq_merge.cc:18: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/yaggo.o jellyfish/yaggo.cpp /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/square_binary_matrix.lo jellyfish/square_binary_matrix.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/square_binary_matrix.cc -fPIC -DPIC -o jellyfish/.libs/square_binary_matrix.o In file included from ./jellyfish/square_binary_matrix.hpp:27, from jellyfish/square_binary_matrix.cc:21: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]': ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]': ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::SingularMatrix]': jellyfish/square_binary_matrix.cc:93:2: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' In file included from jellyfish/square_binary_matrix.cc:21: ./jellyfish/square_binary_matrix.hpp: In function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)': ./jellyfish/square_binary_matrix.hpp:46:12: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 46 | return res; | ^~~ ./jellyfish/square_binary_matrix.hpp: In member function 'void SquareBinaryMatrix::alloc_columns()': ./jellyfish/square_binary_matrix.hpp:55:13: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 55 | columns = first_alloc(size); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from jellyfish/square_binary_matrix.cc:20: ./jellyfish/misc.hpp: In member function 'SquareBinaryMatrix SquareBinaryMatrix::inverse() const': ./jellyfish/misc.hpp:106:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 106 | Tptr ptr; | ^~~ jellyfish/square_binary_matrix.cc:110:19: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 110 | pivot.columns[j] ^= pivot.columns[i]; | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/square_binary_matrix.cc -o jellyfish/square_binary_matrix.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/err.lo jellyfish/err.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/err.cc -fPIC -DPIC -o jellyfish/.libs/err.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/err.cc -o jellyfish/err.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/misc.lo jellyfish/misc.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/misc.cc -fPIC -DPIC -o jellyfish/.libs/misc.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/misc.cc -o jellyfish/misc.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/storage.lo jellyfish/storage.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/storage.cc -fPIC -DPIC -o jellyfish/.libs/storage.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/storage.cc -o jellyfish/storage.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/thread_exec.lo jellyfish/thread_exec.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/thread_exec.cc -fPIC -DPIC -o jellyfish/.libs/thread_exec.o In file included from jellyfish/thread_exec.hpp:26, from jellyfish/thread_exec.cc:17: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = thread_exec::Error]': jellyfish/thread_exec.cc:28:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/thread_exec.cc -o jellyfish/thread_exec.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/time.lo jellyfish/time.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/time.cc -fPIC -DPIC -o jellyfish/.libs/time.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/time.cc -o jellyfish/time.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/file_parser.lo jellyfish/file_parser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/file_parser.cc -fPIC -DPIC -o jellyfish/.libs/file_parser.o In file included from jellyfish/file_parser.cc:17: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]': jellyfish/file_parser.cc:33:5: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/file_parser.cc -o jellyfish/file_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/read_parser.lo jellyfish/read_parser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/read_parser.cc -fPIC -DPIC -o jellyfish/.libs/read_parser.o In file included from ./jellyfish/file_parser.hpp:24, from ./jellyfish/read_parser.hpp:20, from jellyfish/read_parser.cc:17: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]': jellyfish/read_parser.cc:30:5: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/read_parser.cc -o jellyfish/read_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_read.lo jellyfish/parse_read.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_read.cc -fPIC -DPIC -o jellyfish/.libs/parse_read.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_read.cc -o jellyfish/parse_read.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/half.lo jellyfish/half.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/half.cpp -fPIC -DPIC -o jellyfish/.libs/half.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/half.cpp -o jellyfish/half.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mapped_file.lo jellyfish/mapped_file.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/mapped_file.cc -fPIC -DPIC -o jellyfish/.libs/mapped_file.o In file included from ./jellyfish/mapped_file.hpp:29, from jellyfish/mapped_file.cc:17: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = mapped_file::ErrorMMap]': ./jellyfish/mapped_file.hpp:46:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/mapped_file.cc -o jellyfish/mapped_file.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_dna.lo jellyfish/parse_dna.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_dna.cc -fPIC -DPIC -o jellyfish/.libs/parse_dna.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_dna.cc -o jellyfish/parse_dna.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_quake.lo jellyfish/parse_quake.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_quake.cc -fPIC -DPIC -o jellyfish/.libs/parse_quake.o In file included from ./jellyfish/double_fifo_input.hpp:23, from ./jellyfish/parse_quake.hpp:22, from jellyfish/parse_quake.cc:17: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::double_fifo_input::Error]': ./jellyfish/double_fifo_input.hpp:101:7: required from 'jellyfish::double_fifo_input::double_fifo_input(long unsigned int) [with T = jellyfish::seq_qual_parser::sequence_t]' jellyfish/parse_quake.cc:27:40: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]': ./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array::resize() [with T = char]' ./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]' ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_quake.cc -o jellyfish/parse_quake.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_qual_dna.lo jellyfish/parse_qual_dna.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_qual_dna.cc -fPIC -DPIC -o jellyfish/.libs/parse_qual_dna.o In file included from ./jellyfish/double_fifo_input.hpp:23, from ./jellyfish/parse_qual_dna.hpp:22, from jellyfish/parse_qual_dna.cc:17: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::double_fifo_input::Error]': ./jellyfish/double_fifo_input.hpp:101:7: required from 'jellyfish::double_fifo_input::double_fifo_input(long unsigned int) [with T = jellyfish::seq_qual_parser::sequence_t]' jellyfish/parse_qual_dna.cc:27:55: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]': ./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array::resize() [with T = char]' ./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]' ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_qual_dna.cc -o jellyfish/parse_qual_dna.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/sequence_parser.lo jellyfish/sequence_parser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/sequence_parser.cc -fPIC -DPIC -o jellyfish/.libs/sequence_parser.o In file included from ./jellyfish/sequence_parser.hpp:21, from jellyfish/sequence_parser.cc:18: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]': jellyfish/sequence_parser.cc:32:5: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/sequence_parser.cc -o jellyfish/sequence_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/seq_qual_parser.lo jellyfish/seq_qual_parser.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/seq_qual_parser.cc -fPIC -DPIC -o jellyfish/.libs/seq_qual_parser.o In file included from ./jellyfish/seq_qual_parser.hpp:21, from jellyfish/seq_qual_parser.cc:17: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]': jellyfish/seq_qual_parser.cc:31:5: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::fastq_seq_qual_parser::FastqSeqQualParserError]': jellyfish/seq_qual_parser.cc:47:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = jellyfish::simple_growing_array::SimpleGrowingArrayError]': ./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array::resize() [with T = char]' ./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]' ./jellyfish/seq_qual_parser.hpp:53:41: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/seq_qual_parser.cc -o jellyfish/seq_qual_parser.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/backtrace.lo jellyfish/backtrace.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/backtrace.cc -fPIC -DPIC -o jellyfish/.libs/backtrace.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/backtrace.cc -o jellyfish/backtrace.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/floats.lo jellyfish/floats.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/floats.cc -fPIC -DPIC -o jellyfish/.libs/floats.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/floats.cc -o jellyfish/floats.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dbg.lo jellyfish/dbg.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dbg.cc -fPIC -DPIC -o jellyfish/.libs/dbg.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dbg.cc -o jellyfish/dbg.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/allocators_mmap.lo jellyfish/allocators_mmap.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/allocators_mmap.cc -fPIC -DPIC -o jellyfish/.libs/allocators_mmap.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/allocators_mmap.cc -o jellyfish/allocators_mmap.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dna_codes.lo jellyfish/dna_codes.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dna_codes.cc -fPIC -DPIC -o jellyfish/.libs/dna_codes.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dna_codes.cc -o jellyfish/dna_codes.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:1:0 -Wl,-z,relro -Wl,-z,now -o libjellyfish-1.1.la -rpath /usr/lib/x86_64-linux-gnu jellyfish/square_binary_matrix.lo jellyfish/err.lo jellyfish/misc.lo jellyfish/storage.lo jellyfish/thread_exec.lo jellyfish/time.lo jellyfish/file_parser.lo jellyfish/read_parser.lo jellyfish/parse_read.lo jellyfish/half.lo jellyfish/mapped_file.lo jellyfish/parse_dna.lo jellyfish/parse_quake.lo jellyfish/parse_qual_dna.lo jellyfish/sequence_parser.lo jellyfish/seq_qual_parser.lo jellyfish/backtrace.lo jellyfish/floats.lo jellyfish/dbg.lo jellyfish/allocators_mmap.lo jellyfish/dna_codes.lo libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/10/crtbeginS.o jellyfish/.libs/square_binary_matrix.o jellyfish/.libs/err.o jellyfish/.libs/misc.o jellyfish/.libs/storage.o jellyfish/.libs/thread_exec.o jellyfish/.libs/time.o jellyfish/.libs/file_parser.o jellyfish/.libs/read_parser.o jellyfish/.libs/parse_read.o jellyfish/.libs/half.o jellyfish/.libs/mapped_file.o jellyfish/.libs/parse_dna.o jellyfish/.libs/parse_quake.o jellyfish/.libs/parse_qual_dna.o jellyfish/.libs/sequence_parser.o jellyfish/.libs/seq_qual_parser.o jellyfish/.libs/backtrace.o jellyfish/.libs/floats.o jellyfish/.libs/dbg.o jellyfish/.libs/allocators_mmap.o jellyfish/.libs/dna_codes.o -L/usr/lib/gcc/x86_64-linux-gnu/10 -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/10/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/10/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/crtn.o -g -O3 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libjellyfish-1.1.so.1 -o .libs/libjellyfish-1.1.so.1.0.1 libtool: link: (cd ".libs" && rm -f "libjellyfish-1.1.so.1" && ln -s "libjellyfish-1.1.so.1.0.1" "libjellyfish-1.1.so.1") libtool: link: (cd ".libs" && rm -f "libjellyfish-1.1.so" && ln -s "libjellyfish-1.1.so.1.0.1" "libjellyfish-1.1.so") libtool: link: ar cr .libs/libjellyfish-1.1.a jellyfish/square_binary_matrix.o jellyfish/err.o jellyfish/misc.o jellyfish/storage.o jellyfish/thread_exec.o jellyfish/time.o jellyfish/file_parser.o jellyfish/read_parser.o jellyfish/parse_read.o jellyfish/half.o jellyfish/mapped_file.o jellyfish/parse_dna.o jellyfish/parse_quake.o jellyfish/parse_qual_dna.o jellyfish/sequence_parser.o jellyfish/seq_qual_parser.o jellyfish/backtrace.o jellyfish/floats.o jellyfish/dbg.o jellyfish/allocators_mmap.o jellyfish/dna_codes.o libtool: link: ranlib .libs/libjellyfish-1.1.a libtool: link: ( cd ".libs" && rm -f "libjellyfish-1.1.la" && ln -s "../libjellyfish-1.1.la" "libjellyfish-1.1.la" ) /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,--as-needed -latomic -Wl,-z,relro -Wl,-z,now -o bin/jellyfish jellyfish/jellyfish.o jellyfish/stats_main.o jellyfish/hash_merge.o jellyfish/mer_counter.o jellyfish/histo_main.o jellyfish/dump_main.o jellyfish/query_main.o jellyfish/dump_fastq_main.o jellyfish/histo_fastq_main.o jellyfish/cite.o jellyfish/hash_fastq_merge.o jellyfish/yaggo.o libjellyfish-1.1.la libtool: link: g++ -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--as-needed -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/jellyfish jellyfish/jellyfish.o jellyfish/stats_main.o jellyfish/hash_merge.o jellyfish/mer_counter.o jellyfish/histo_main.o jellyfish/dump_main.o jellyfish/query_main.o jellyfish/dump_fastq_main.o jellyfish/histo_fastq_main.o jellyfish/cite.o jellyfish/hash_fastq_merge.o jellyfish/yaggo.o -lpthread -latomic ./.libs/libjellyfish-1.1.so make[3]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/generate_sequence.o jellyfish/generate_sequence.cc In file included from jellyfish/generate_sequence.cc:22: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]': ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]': ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' In file included from jellyfish/generate_sequence.cc:24: ./jellyfish/square_binary_matrix.hpp: In function 'int main(int, char**)': ./jellyfish/square_binary_matrix.hpp:87:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 87 | free(columns); | ~~~~^~~~~~~~~ In file included from jellyfish/generate_sequence.cc:23: ./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here 106 | Tptr ptr; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mersenne.o jellyfish/mersenne.cpp /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,-z,relro -Wl,-z,now -o bin/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o libjellyfish-1.1.la libtool: link: g++ -g -O3 -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o -lpthread ./.libs/libjellyfish-1.1.so g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_offsets_key_value.o `test -f 'unit_tests/test_offsets_key_value.cc' || echo './'`unit_tests/test_offsets_key_value.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_simple_circular_buffer.o `test -f 'unit_tests/test_simple_circular_buffer.cc' || echo './'`unit_tests/test_simple_circular_buffer.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_square_binary_matrix.o `test -f 'unit_tests/test_square_binary_matrix.cc' || echo './'`unit_tests/test_square_binary_matrix.cc unit_tests/test_square_binary_matrix.cc: In member function 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()': unit_tests/test_square_binary_matrix.cc:81:48: warning: catching polymorphic type 'class SquareBinaryMatrix::SingularMatrix' by value [-Wcatch-value=] 81 | } catch(SquareBinaryMatrix::SingularMatrix e) { | ^ In file included from ./jellyfish/square_binary_matrix.hpp:27, from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]': ./jellyfish/square_binary_matrix.hpp:45:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] 123 | ~raise_t() { throw err_t(oss.str()); } | ^~~~~~~~~~~~~~~~~~~~~~ ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' ./jellyfish/err.hpp: In instantiation of 'err::raise_t::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]': ./jellyfish/square_binary_matrix.hpp:54:7: required from here ./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate] ./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept' In file included from unit_tests/test_square_binary_matrix.cc:3: ./jellyfish/square_binary_matrix.hpp: In function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)': ./jellyfish/square_binary_matrix.hpp:46:12: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized] 46 | return res; | ^~~ g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest -I./unit_tests/gtest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_main_a-gtest_main.o `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest -I./unit_tests/gtest/include -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_a-gtest-all.o `test -f 'unit_tests/gtest/src/gtest-all.cc' || echo './'`unit_tests/gtest/src/gtest-all.cc In file included from /usr/include/string.h:495, from ./unit_tests/gtest/include/gtest/internal/gtest-port.h:195, from ./unit_tests/gtest/include/gtest/internal/gtest-internal.h:40, from ./unit_tests/gtest/include/gtest/gtest.h:57, from unit_tests/gtest/src/gtest-all.cc:39: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'const char* testing::internal::posix::StrNCpy(char*, const char*, size_t)' at ./unit_tests/gtest/include/gtest/internal/gtest-port.h:1615:17, inlined from 'char* testing::internal::CloneString(const char*, size_t)' at ./unit_tests/gtest/src/gtest.cc:840:19, inlined from 'static const char* testing::internal::String::CloneCString(const char*)' at ./unit_tests/gtest/src/gtest.cc:851:39: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from unit_tests/gtest/src/gtest-all.cc:42: ./unit_tests/gtest/src/gtest.cc: In static member function 'static const char* testing::internal::String::CloneCString(const char*)': ./unit_tests/gtest/src/gtest.cc:851:39: note: length computed here 851 | NULL : CloneString(c_str, strlen(c_str)); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ rm -f libgtest.a ar cru libgtest.a unit_tests/gtest/src/libgtest_a-gtest-all.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest.a rm -f libgtest_main.a ar cru libgtest_main.a unit_tests/gtest/src/libgtest_main_a-gtest_main.o libgtest.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgtest_main.a /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,-z,relro -Wl,-z,now -o bin/test_all unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_square_binary_matrix.o libgtest_main.a libgtest.a libjellyfish-1.1.la libtool: link: g++ -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/test_all unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_square_binary_matrix.o -lpthread libgtest_main.a libgtest.a ./.libs/libjellyfish-1.1.so make[2]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11' make[1]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/jellyfish1-1.1.11' # dh_auto_test && true echo "****************************************************** do not test for the moment ******************************************************" ****************************************************** do not test for the moment ****************************************************** make[1]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/jellyfish1-1.1.11' dh_auto_install --destdir=debian/tmp make -j1 install DESTDIR=/build/reproducible-path/jellyfish1-1.1.11/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/reproducible-path/jellyfish1-1.1.11' make[3]: Entering directory '/build/reproducible-path/jellyfish1-1.1.11' /bin/mkdir -p '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-1.1.la '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.so.1.0.1 /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.so.1.0.1 libtool: install: (cd /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so.1 || { rm -f libjellyfish-1.1.so.1 && ln -s libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so.1; }; }) libtool: install: (cd /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so || { rm -f libjellyfish-1.1.so && ln -s libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.lai /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.la libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.a /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.a libtool: install: chmod 644 /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.a libtool: install: ranlib /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-1.1.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/bin/jellyfish /bin/mkdir -p '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/include/jellyfish-1.1.11/jellyfish' /usr/bin/install -c -m 644 jellyfish/allocators_malloc.hpp jellyfish/allocators_mmap.hpp jellyfish/allocators_shm.hpp jellyfish/atomic_gcc.hpp jellyfish/compacted_dumper.hpp jellyfish/compacted_hash.hpp jellyfish/concurrent_queues.hpp jellyfish/direct_indexing_array.hpp jellyfish/direct_sorted_dumper.hpp jellyfish/divisor.hpp jellyfish/dumper.hpp jellyfish/hash_function.hpp jellyfish/hash.hpp jellyfish/heap.hpp jellyfish/invertible_hash_array.hpp jellyfish/locking_hash_counters.hpp jellyfish/locks_pthread.hpp jellyfish/mapped_file.hpp jellyfish/mer_counting.hpp jellyfish/err.hpp jellyfish/misc.hpp jellyfish/offsets_key_value.hpp jellyfish/reversible_hash_function.hpp jellyfish/sorted_dumper.hpp jellyfish/square_binary_matrix.hpp jellyfish/storage.hpp jellyfish/thread_exec.hpp jellyfish/time.hpp jellyfish/token_ring.hpp jellyfish/raw_dumper.hpp jellyfish/capped_integer.hpp jellyfish/aligned_values_array.hpp jellyfish/fastq_dumper.hpp jellyfish/floats.hpp jellyfish/circular_buffer.hpp jellyfish/counter.hpp jellyfish/parse_quake.hpp jellyfish/parse_dna.hpp jellyfish/parse_qual_dna.hpp jellyfish/file_parser.hpp '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/include/jellyfish-1.1.11/jellyfish' /usr/bin/install -c -m 644 jellyfish/sequence_parser.hpp jellyfish/seq_qual_parser.hpp jellyfish/double_fifo_input.hpp jellyfish/read_parser.hpp jellyfish/parse_read.hpp jellyfish/simple_growing_array.hpp jellyfish/toFloat.h jellyfish/eLut.h jellyfish/dbg.hpp jellyfish/half.h jellyfish/backtrace.hpp jellyfish/dna_codes.hpp jellyfish/simple_circular_buffer.hpp '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/include/jellyfish-1.1.11/jellyfish' /bin/mkdir -p '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/share/man/man1/jellyfish.1' /bin/mkdir -p '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-1.1.pc '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' make[3]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11' make[2]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11' make[1]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/jellyfish1-1.1.11' mkdir -p debian/tmp/usr/lib/jellyfish1 mv debian/tmp/usr/bin/* debian/tmp/usr/lib/jellyfish1 dh_install find debian -name "*.a" -delete find debian -name "*.la" -delete find debian -name "*.so" -delete find debian -name "pkgconfig" -type d | xargs rm -rf # there is no development package for this version any more - remove header files to keep dh_missing happy rm -rf debian/tmp/usr/include/jellyfish* make[1]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/jellyfish1-1.1.11' dh_installman mv debian/jellyfish1/usr/share/man/man1/jellyfish.1 debian/jellyfish1/usr/share/man/man1/jellyfish1.1 make[1]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11' dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: symbol pthread_cancel used by debian/jellyfish1/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.so.1.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol pthread_create used by debian/jellyfish1/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.so.1.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol pthread_join used by debian/jellyfish1/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.so.1.0.1 found in none of the libraries dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'jellyfish1' in '../jellyfish1_1.1.11-5_amd64.deb'. dpkg-deb: building package 'jellyfish1-dbgsym' in '../jellyfish1-dbgsym_1.1.11-5_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../jellyfish1_1.1.11-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3667473 and its subdirectories I: Current time: Sat Jul 27 23:10:03 -12 2024 I: pbuilder-time-stamp: 1722165003 Sun Jul 28 11:10:04 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Sun Jul 28 11:10:04 UTC 2024 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Sun Jul 28 11:11:48 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Sun Jul 28 11:11:49 UTC 2024 I: jellyfish1_1.1.11-5_amd64.changes: Format: 1.8 Date: Thu, 26 Nov 2020 07:52:51 +0100 Source: jellyfish1 Binary: jellyfish1 jellyfish1-dbgsym Architecture: amd64 Version: 1.1.11-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: jellyfish1 - count k-mers in DNA sequences Changes: jellyfish1 (1.1.11-5) unstable; urgency=medium . * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine- update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Use secure URI in Homepage field. Checksums-Sha1: 62b8a8507a7cc5fc6ef1288c8bd93b6685ee5d5d 1151044 jellyfish1-dbgsym_1.1.11-5_amd64.deb e1204e7c6544031a41a72ef319c9e95f7e4bc01f 5312 jellyfish1_1.1.11-5_amd64.buildinfo 79d0de2e8cbc6ec119e7b2cb6966bbc88dada1fc 130472 jellyfish1_1.1.11-5_amd64.deb Checksums-Sha256: a31b52415f01161b392d99260a7a7acf2200570e6d11830cb4a6abdcaef76611 1151044 jellyfish1-dbgsym_1.1.11-5_amd64.deb d1f04488645d6c76dfa0750bfabad87971e1998435cb19caaf148855059d1544 5312 jellyfish1_1.1.11-5_amd64.buildinfo 75ad9b06bac64c2218f886ef4c1957121a1e41123fd0599e9730bfbebee8d342 130472 jellyfish1_1.1.11-5_amd64.deb Files: 08f405bab0f9798671608cb8859d040b 1151044 debug optional jellyfish1-dbgsym_1.1.11-5_amd64.deb 2a138a0c19798f7e5bc62347a12f53d0 5312 science optional jellyfish1_1.1.11-5_amd64.buildinfo 60ae13112b34f8742740aa8d8356dd70 130472 science optional jellyfish1_1.1.11-5_amd64.deb Sun Jul 28 11:11:50 UTC 2024 I: diffoscope 272 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_5-14781.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ZhBxk5K5/jellyfish1_1.1.11-5.diffoscope.html --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ZhBxk5K5/b1/jellyfish1_1.1.11-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ZhBxk5K5/b2/jellyfish1_1.1.11-5_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.307s) 0.307s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.033s) 0.033s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 615ms CPU time consumed: 617ms Sun Jul 28 11:11:51 UTC 2024 I: diffoscope 272 found no differences in the changes files, and a .buildinfo file also exists. Sun Jul 28 11:11:51 UTC 2024 I: jellyfish1 from bullseye built successfully and reproducibly on amd64. Sun Jul 28 11:11:52 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Jul 28 11:11:52 UTC 2024 I: Submitting 8.0K b1/jellyfish1_1.1.11-5_amd64.buildinfo.asc Sun Jul 28 11:11:53 UTC 2024 I: Submitting 8.0K b2/jellyfish1_1.1.11-5_amd64.buildinfo.asc Sun Jul 28 11:11:54 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jul 28 11:11:54 UTC 2024 I: Done submitting .buildinfo files. Sun Jul 28 11:11:54 UTC 2024 I: Removing signed jellyfish1_1.1.11-5_amd64.buildinfo.asc files: removed './b1/jellyfish1_1.1.11-5_amd64.buildinfo.asc' removed './b2/jellyfish1_1.1.11-5_amd64.buildinfo.asc'