Sun May 12 20:58:08 UTC 2024 I: starting to build jellyfish1/trixie/arm64 on jenkins on '2024-05-12 20:57' Sun May 12 20:58:08 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_18/40525/console.log Sun May 12 20:58:08 UTC 2024 I: Downloading source for trixie/jellyfish1=1.1.11-9 --2024-05-12 20:58:08-- http://deb.debian.org/debian/pool/main/j/jellyfish1/jellyfish1_1.1.11-9.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2170 (2.1K) [text/prs.lines.tag] Saving to: ‘jellyfish1_1.1.11-9.dsc’ 0K .. 100% 277M=0s 2024-05-12 20:58:08 (277 MB/s) - ‘jellyfish1_1.1.11-9.dsc’ saved [2170/2170] Sun May 12 20:58:08 UTC 2024 I: jellyfish1_1.1.11-9.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: jellyfish1 Binary: jellyfish1 Architecture: amd64 arm64 loong64 mips64el ppc64el hppa ia64 kfreebsd-amd64 riscv64 Version: 1.1.11-9 Maintainer: Debian Med Packaging Team Uploaders: Shaun Jackman , Andreas Tille Homepage: https://www.cbcb.umd.edu/software/jellyfish/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/jellyfish1 Vcs-Git: https://salsa.debian.org/med-team/jellyfish1.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: jellyfish1 deb science optional arch=amd64,arm64,loong64,mips64el,ppc64el,hppa,ia64,kfreebsd-amd64,riscv64 Checksums-Sha1: 8bd6a7b382e94d37adfddd916dec2b0e36f840fd 1067138 jellyfish1_1.1.11.orig.tar.gz 7712fe8f75d7792bc4a121a9da68900bc15011ce 6376 jellyfish1_1.1.11-9.debian.tar.xz Checksums-Sha256: 496645d96b08ba35db1f856d857a159798c73cbc1eccb852ef1b253d1678c8e2 1067138 jellyfish1_1.1.11.orig.tar.gz 2248b754a1afcc2e6e2df8860ca3a1d7241a839f958735538c4712146a322884 6376 jellyfish1_1.1.11-9.debian.tar.xz Files: dc994ea8b0896156500ea8c648f24846 1067138 jellyfish1_1.1.11.orig.tar.gz bce2ccdb4cdb2adda667c22486945eab 6376 jellyfish1_1.1.11-9.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmVp0bMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH8sRAAmJmiBBfELUQIzOavhkZehFPE1Q30ZE7l zruegCMfB3+QfT6jI7L2NHXY9rJcW4iqbck27Bo303n9oToP4P5gyo/uLP3awDP+ fVzjTrZKC/2+YI+RSJ7jwPGjqi/ZVzuRUGkFstjCBDMcvQzNix1ntA4F2UnL8B+M oe83DFUybbsw0d8fJArnTF4UYUOGnsrAO+0/09AHcDkU/iFcrJ7Z+UqYJcjLZgXE hwJDv5zEGAObYoig+nr2H/apffw5saJ6giZcBJs+3lD9paMPrIwJuloLWd8b81YB iWB53uI1s4f2hqjIACPMZJ1Wn4grpFwe2eOlRNGIWufYqEVfOW8ocQLyXdNxScpQ 1C6y4G5Ma//lKD7FMBkyY5M67pLGEqMtCu8tjU2dW/hjD9vUMC5+fu6vZVRl7bji XwsBUcwydb4NopIaSfqOhz2gIcx1v1SmMtZAVdStkcMUFMpiaYNkOiBp6tMzEh16 cztCwyNbpXnilmC0es4+FGEJtU0W6+BCF7XeTaBnhK8pF2D3cuKh41/Mup8Gg8Vb hcXLPgvn7MgnOig3rY6m7AeIfb8zNncup0zrgs2tgZsI+OrMv5bESzNJgbsmJs1q au10oVv+raUQ1IhC/F00fIP5aie280TbELRl+R18DgVPUqp+JuqjHx1b37JkqpPJ eFGNfM8rMqY= =Agw5 -----END PGP SIGNATURE----- Sun May 12 20:58:08 UTC 2024 I: Checking whether the package is not for us Sun May 12 20:58:08 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sun May 12 20:58:08 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sun May 12 21:00:20 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 12 08:58:11 -12 2024 I: pbuilder-time-stamp: 1715547491 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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_1.1.11-9.dsc] I: copying [./jellyfish1_1.1.11.orig.tar.gz] I: copying [./jellyfish1_1.1.11-9.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Dec 1 12:29:39 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./jellyfish1_1.1.11-9.dsc: no acceptable signature found 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_1.1.11-9.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 dpkg-source: info: applying autoconf.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1837930/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='9976aaa021744bc3aa4e6ccdb4668ecf' 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='1837930' 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.qBDPnY8F/pbuilderrc_9oBj --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qBDPnY8F/b1 --logfile b1/build.log jellyfish1_1.1.11-9.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 11 11:23 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1837930/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: arm64 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 ... 19745 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} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{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, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 18.7 MB of archives. After unpacking 75.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Fetched 18.7 MB in 0s (137 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19745 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-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 .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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_1.1.11-9_source.changes dpkg-buildpackage: info: source package jellyfish1 dpkg-buildpackage: info: source version 1.1.11-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead 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:8: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:8: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:8: the top level configure.ac:61: warning: The macro `AC_HELP_STRING' is obsolete. configure.ac:61: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:61: the top level configure.ac:8: installing './compile' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=aarch64-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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... 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... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/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 aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file 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... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.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) 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 the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) 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) 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 for g++ options needed to detect all undeclared functions... none needed checking whether strerror_r is declared... yes checking whether strerror_r returns char *... yes checking for execinfo.h... 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 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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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; 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: In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:173:9, inlined 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]' at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/stats_main.cc:25: ./jellyfish/misc.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/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:173:36, inlined 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]' at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.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/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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:189:38: 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/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: In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'SquareBinaryMatrix jellyfish::compacted_hash::reader::get_hash_matrix() const [with key_t = long unsigned int; val_t = long unsigned int]' at ./jellyfish/compacted_hash.hpp:245:59, inlined from 'int merge_main(int, char**)' at jellyfish/hash_merge.cc:138:69: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/hash_merge.cc:33: ./jellyfish/misc.hpp: In function 'int merge_main(int, char**)': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'SquareBinaryMatrix jellyfish::compacted_hash::reader::get_hash_inverse_matrix() const [with key_t = long unsigned int; val_t = long unsigned int]' at ./jellyfish/compacted_hash.hpp:246:67, inlined from 'int merge_main(int, char**)' at jellyfish/hash_merge.cc:140:35: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In function 'int merge_main(int, char**)': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'SquareBinaryMatrix jellyfish::compacted_hash::reader::get_hash_matrix() const [with key_t = long unsigned int; val_t = long unsigned int]' at ./jellyfish/compacted_hash.hpp:245:59, inlined from 'int merge_main(int, char**)' at jellyfish/hash_merge.cc:135:45: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In function 'int merge_main(int, char**)': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'SquareBinaryMatrix jellyfish::compacted_hash::reader::get_hash_inverse_matrix() const [with key_t = long unsigned int; val_t = long unsigned int]' at ./jellyfish/compacted_hash.hpp:246:67, inlined from 'int merge_main(int, char**)' at jellyfish/hash_merge.cc:136:61: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In function 'int merge_main(int, char**)': ./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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:149:22: 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 { | ^~~~~~ ./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/hash.hpp:31, from ./jellyfish/mer_counting.hpp:28: In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(int)' at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from 'void jellyfish::direct_indexing::array::write_ary_header(std::ostream*) const [with key_t = long unsigned int; val_t = jellyfish::capped_integer; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/direct_indexing_array.hpp:52:28, inlined from 'void jellyfish::compacted_hash::writer::write_header(std::ostream*) const [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>]' at ./jellyfish/compacted_hash.hpp:121:30, inlined from 'void jellyfish::direct_sorted_dumper::_dump() [with storage_t = jellyfish::direct_indexing::array, atomic::gcc, allocators::mmap>; atomic_t = atomic::gcc]' at ./jellyfish/direct_sorted_dumper.hpp:101:39: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ 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: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'void jellyfish::invertible_hash::array::set_matrix(SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:187:21, inlined from 'void jellyfish::invertible_hash::array::set_matrix(SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:183:12: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.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/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(int)' at ./jellyfish/square_binary_matrix.hpp:61:62, inlined 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]' at ./jellyfish/invertible_hash_array.hpp:112:9: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In constructor '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]': ./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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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; 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: In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:173:9, inlined 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]' at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/histo_main.cc:26: ./jellyfish/misc.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/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:173:36, inlined 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]' at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.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/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'SquareBinaryMatrix jellyfish::compacted_hash::query::get_hash_matrix() const [with key_t = long unsigned int; val_t = long unsigned int]' at ./jellyfish/compacted_hash.hpp:370:59, inlined from 'int histo_main(int, char**)' at jellyfish/histo_main.cc:121:60: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In function 'int histo_main(int, char**)': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'SquareBinaryMatrix jellyfish::compacted_hash::query::get_hash_inverse_matrix() const [with key_t = long unsigned int; val_t = long unsigned int]' at ./jellyfish/compacted_hash.hpp:371:67, inlined from 'int histo_main(int, char**)' at jellyfish/histo_main.cc:122:68: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In function 'int histo_main(int, char**)': ./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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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; 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: In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:173:9, inlined 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]' at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/dump_main.cc:25: ./jellyfish/misc.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/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:173:36, inlined 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]' at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.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/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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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; 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: In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:173:9, inlined 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]' at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/query_main.cc:23: ./jellyfish/misc.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/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:173:36, inlined 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]' at ./jellyfish/raw_dumper.hpp:199:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.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/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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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: In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:173:9, inlined from 'jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(char*, char*, size_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/aligned_values_array.hpp:49:9, inlined from 'static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]' at ./jellyfish/fastq_dumper.hpp:122:14: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/dump_fastq_main.cc:26: ./jellyfish/misc.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/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:173:36, inlined from 'jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(char*, char*, size_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/aligned_values_array.hpp:49:9, inlined from 'static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]' at ./jellyfish/fastq_dumper.hpp:122:14: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.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/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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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: In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:173:9, inlined from 'jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(char*, char*, size_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/aligned_values_array.hpp:49:9, inlined from 'static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]' at ./jellyfish/fastq_dumper.hpp:122:14: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/histo_fastq_main.cc:27: ./jellyfish/misc.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/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:173:36, inlined from 'jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(char*, char*, size_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/aligned_values_array.hpp:49:9, inlined from 'static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]' at ./jellyfish/fastq_dumper.hpp:122:14: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.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/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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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:49:12: 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:41:9: 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: In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:173:9, inlined from 'jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(char*, char*, size_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/aligned_values_array.hpp:49:9, inlined from 'static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]' at ./jellyfish/fastq_dumper.hpp:122:14: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/hash_fastq_merge.cc:18: ./jellyfish/misc.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/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'jellyfish::invertible_hash::array::array(char*, size_t, uint_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:173:36, inlined from 'jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(char*, char*, size_t, uint_t, uint_t, size_t*, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/aligned_values_array.hpp:49:9, inlined from 'static storage_t* jellyfish::fastq_hash::raw_dumper::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array]' at ./jellyfish/fastq_dumper.hpp:122:14: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.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/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(int)' at ./jellyfish/square_binary_matrix.hpp:61:62, inlined 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]' at ./jellyfish/invertible_hash_array.hpp:112:9: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In constructor '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]': ./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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(int)' at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from 'SquareBinaryMatrix SquareBinaryMatrix::transpose() const' at jellyfish/square_binary_matrix.cc:52:30: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/square_binary_matrix.cc:20: ./jellyfish/misc.hpp: In member function 'SquareBinaryMatrix SquareBinaryMatrix::transpose() const': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'void SquareBinaryMatrix::alloc_columns()' at ./jellyfish/square_binary_matrix.hpp:55:26, inlined from 'void SquareBinaryMatrix::load(std::istream*)' at jellyfish/square_binary_matrix.cc:143:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function 'void SquareBinaryMatrix::load(std::istream*)': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'void SquareBinaryMatrix::alloc_columns()' at ./jellyfish/square_binary_matrix.hpp:55:26, inlined from 'size_t SquareBinaryMatrix::read(const char*)' at jellyfish/square_binary_matrix.cc:154:16: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function 'size_t SquareBinaryMatrix::read(const char*)': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(int)' at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from 'SquareBinaryMatrix SquareBinaryMatrix::operator*(const SquareBinaryMatrix&) const' at jellyfish/square_binary_matrix.cc:65:30: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function 'SquareBinaryMatrix SquareBinaryMatrix::operator*(const SquareBinaryMatrix&) const': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'SquareBinaryMatrix SquareBinaryMatrix::inverse() const' at jellyfish/square_binary_matrix.cc:80:33: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function 'SquareBinaryMatrix SquareBinaryMatrix::inverse() const': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(int)' at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from 'SquareBinaryMatrix SquareBinaryMatrix::inverse() const' at jellyfish/square_binary_matrix.cc:81:30: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function 'SquareBinaryMatrix SquareBinaryMatrix::inverse() const': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c jellyfish/half.cpp -fPIC -DPIC -o jellyfish/.libs/half.o In file included from jellyfish/half.cpp:48: ./jellyfish/half.h: In constructor 'half::half(float)': ./jellyfish/half.h:471:22: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 471 | register int e = (x.i >> 23) & 0x000001ff; | ^ ./jellyfish/half.h:482:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 482 | register int m = x.i & 0x007fffff; | ^ jellyfish/half.cpp: In static member function 'static short int half::convert(int)': jellyfish/half.cpp:98:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 98 | register int s = (i >> 16) & 0x00008000; | ^ jellyfish/half.cpp:99:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 99 | register int e = ((i >> 23) & 0x000000ff) - (127 - 15); | ^ jellyfish/half.cpp:100:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 100 | register int m = i & 0x007fffff; | ^ libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c jellyfish/sequence_parser.cc -fPIC -DPIC -o jellyfish/.libs/sequence_parser.o jellyfish/sequence_parser.cc: In member function 'virtual bool jellyfish::fasta_sequence_parser::parse(char*, char**)': jellyfish/sequence_parser.cc:43:5: warning: case label value is less than minimum value for type [-Wswitch-outside-range] 43 | case _eof: | ^~~~ 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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -version-info 1:1:0 -Wl,-z,relro -Wl,-z,now -o libjellyfish-1.1.la -rpath /usr/lib/aarch64-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/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/13/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/aarch64-linux-gnu/13 -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/13/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/crtn.o -g -O3 -g -O2 -fstack-protector-strong -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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: In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(int)' at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from 'int main(int, char**)' at jellyfish/generate_sequence.cc:76:39: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from jellyfish/generate_sequence.cc:23: ./jellyfish/misc.hpp: In function 'int main(int, char**)': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(int)' at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from 'int main(int, char**)' at jellyfish/generate_sequence.cc:76:57: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In function 'int main(int, char**)': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const uint64_t*, int)' at ./jellyfish/square_binary_matrix.hpp:71:80, inlined from 'int main(int, char**)' at jellyfish/generate_sequence.cc:80:13: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In function 'int main(int, char**)': ./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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o jellyfish/mersenne.o jellyfish/mersenne.cpp /bin/bash ./libtool --tag=CXX --mode=link g++ -g -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(int)' at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()' at unit_tests/test_square_binary_matrix.cc:32:34: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ In file included from ./jellyfish/square_binary_matrix.hpp:28: ./jellyfish/misc.hpp: In member function 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(int)' at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()' at unit_tests/test_square_binary_matrix.cc:37:33: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(int)' at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()' at unit_tests/test_square_binary_matrix.cc:38:35: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(int)' at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()' at unit_tests/test_square_binary_matrix.cc:47:31: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()' at unit_tests/test_square_binary_matrix.cc:48:13: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)' at ./jellyfish/square_binary_matrix.hpp:64:74, inlined from 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()' at unit_tests/test_square_binary_matrix.cc:52:32: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()': ./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here 106 | Tptr ptr; | ^~~ In member function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)', inlined from 'SquareBinaryMatrix::SquareBinaryMatrix(int)' at ./jellyfish/square_binary_matrix.hpp:61:62, inlined from 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()' at unit_tests/test_square_binary_matrix.cc:73:32: ./jellyfish/square_binary_matrix.hpp:44:5: warning: '*&ptr' may be used uninitialized [-Wmaybe-uninitialized] 44 | if(!res) | ^~ ./jellyfish/misc.hpp: In member function 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()': ./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 -I./unit_tests/gtest -I./unit_tests/gtest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 ./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: ./unit_tests/gtest/include/gtest/internal/gtest-port.h: In static member function 'static const char* testing::internal::String::CloneCString(const char*)': ./unit_tests/gtest/include/gtest/internal/gtest-port.h:1615:17: 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] 1615 | return strncpy(dest, src, n); | ^ In file included from unit_tests/gtest/src/gtest-all.cc:42: ./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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libjellyfish-1.1.so.1.0.1 libtool: install: (cd /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/libjellyfish-1.1.a libtool: install: chmod 644 /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-1.1.a libtool: install: ranlib /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-1.1.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu' /usr/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/aarch64-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/bin/jellyfish /usr/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' /usr/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' /usr/bin/mkdir -p '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-1.1.pc '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'jellyfish1-dbgsym' in '../jellyfish1-dbgsym_1.1.11-9_arm64.deb'. dpkg-deb: building package 'jellyfish1' in '../jellyfish1_1.1.11-9_arm64.deb'. dpkg-genbuildinfo --build=binary -O../jellyfish1_1.1.11-9_arm64.buildinfo dpkg-genchanges --build=binary -O../jellyfish1_1.1.11-9_arm64.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/1837930 and its subdirectories I: Current time: Sun May 12 09:00:18 -12 2024 I: pbuilder-time-stamp: 1715547618 Sun May 12 21:00:21 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Sun May 12 21:00:21 UTC 2024 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Sun May 12 21:02:34 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Sun May 12 21:02:35 UTC 2024 I: jellyfish1_1.1.11-9_arm64.changes: Format: 1.8 Date: Fri, 01 Dec 2023 11:51:12 +0100 Source: jellyfish1 Binary: jellyfish1 jellyfish1-dbgsym Architecture: arm64 Version: 1.1.11-9 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: jellyfish1 - count k-mers in DNA sequences Closes: 1057127 Changes: jellyfish1 (1.1.11-9) unstable; urgency=medium . * Add support for loongarch64 in d/control Closes: #1057127 * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 70d9499614d57d68095bb5d4ad0b10e33a171c3b 1158528 jellyfish1-dbgsym_1.1.11-9_arm64.deb fcdcede9b15bbcf68f3f7fb5fc8f81e0ca8b4f00 5127 jellyfish1_1.1.11-9_arm64.buildinfo 7f4617249001346775c3c05600828172c95ab746 130048 jellyfish1_1.1.11-9_arm64.deb Checksums-Sha256: 32322a251622e20df3230af6236df55e12f01264c5f574cef9b9428bd17f2abf 1158528 jellyfish1-dbgsym_1.1.11-9_arm64.deb e79555ad1601f4df2f4ab7be20eed320cf014ff7785861f6ec74de20da1129e1 5127 jellyfish1_1.1.11-9_arm64.buildinfo d0ab90f154bb423960b4dd91c258fa1a9d216d9f1c535219d15d1e896c830f3f 130048 jellyfish1_1.1.11-9_arm64.deb Files: fea57b9b420de2fd36e11b3b2e355068 1158528 debug optional jellyfish1-dbgsym_1.1.11-9_arm64.deb 1d0760f83dfe18f2c0a80646e4eb2d81 5127 science optional jellyfish1_1.1.11-9_arm64.buildinfo d167b17c41f1d5905f105f323ed3b6fd 130048 science optional jellyfish1_1.1.11-9_arm64.deb Sun May 12 21:02:36 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_18-40525.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.qBDPnY8F/jellyfish1_1.1.11-9.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.qBDPnY8F/jellyfish1_1.1.11-9.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.qBDPnY8F/jellyfish1_1.1.11-9.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.qBDPnY8F/b1/jellyfish1_1.1.11-9_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.qBDPnY8F/b2/jellyfish1_1.1.11-9_arm64.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: 0.376s) 0.376s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.029s) 0.029s 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: 737ms CPU time consumed: 739ms Sun May 12 21:02:37 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Sun May 12 21:02:37 UTC 2024 I: jellyfish1 from trixie built successfully and reproducibly on arm64. Sun May 12 21:02:39 UTC 2024 I: Submitting .buildinfo files to external archives: Sun May 12 21:02:39 UTC 2024 I: Submitting 8.0K b1/jellyfish1_1.1.11-9_arm64.buildinfo.asc Sun May 12 21:02:39 UTC 2024 I: Submitting 8.0K b2/jellyfish1_1.1.11-9_arm64.buildinfo.asc Sun May 12 21:02:40 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun May 12 21:02:40 UTC 2024 I: Done submitting .buildinfo files. Sun May 12 21:02:40 UTC 2024 I: Removing signed jellyfish1_1.1.11-9_arm64.buildinfo.asc files: removed './b1/jellyfish1_1.1.11-9_arm64.buildinfo.asc' removed './b2/jellyfish1_1.1.11-9_arm64.buildinfo.asc'