I: pbuilder: network access will be disabled during build
I: Current time: Tue Feb 18 01:36:05 +14 2025
I: pbuilder-time-stamp: 1739792165
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-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_1.1.11-10.dsc]
I: copying [./jellyfish1_1.1.11.orig.tar.gz]
I: copying [./jellyfish1_1.1.11-10.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./jellyfish1_1.1.11-10.dsc: unsupported subcommand
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_1.1.11-10.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/1611040/tmp/hooks/D01_modify_environment starting
debug: Running on ionos1-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Feb 17 11:36 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/1611040/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/1611040/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=amd64
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
DIRSTACK=()
DISTRIBUTION=unstable
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=x86_64
HOST_ARCH=amd64
IFS='
'
INVOCATION_ID=1a45ed85d99d4a43b242ef9fc09f71c6
LANG=C
LANGUAGE=et_EE:et
LC_ALL=C
MACHTYPE=x86_64-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=1611040
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.lnQwO2zt/pbuilderrc_d95p --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lnQwO2zt/b2 --logfile b2/build.log jellyfish1_1.1.11-10.dsc'
SUDO_GID=110
SUDO_UID=105
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://46.16.76.132:3128
I: uname -a
Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1611040/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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 ... 19855 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} libtool{a} libuchardet0{a} libunistring5{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 20.6 MB of archives. After unpacking 77.9 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Fetched 20.6 MB in 1s (16.6 MB/s)
Preconfiguring packages ...
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%
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(Reading database ... 90%
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(Reading database ... 100%
(Reading database ... 19855 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:amd64.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ...
Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ...
Unpacking gettext-base (0.23.1-1) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.4-3_amd64.deb ...
Unpacking bsdextrautils (2.40.4-3) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-5_amd64.deb ...
Unpacking m4 (1.4.19-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
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%3a1.17-3_all.deb ...
Unpacking automake (1:1.17-3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ...
Unpacking autopoint (0.23.1-1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ...
Unpacking libdebhelper-perl (13.24.1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.5.4-3_all.deb ...
Unpacking libtool (2.5.4-3) ...
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 libfile-stripnondeterminism-perl.
Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.1-2) ...
Selecting previously unselected package libelf1t64:amd64.
Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ...
Unpacking libelf1t64:amd64 (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ...
Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package libunistring5:amd64.
Preparing to unpack .../23-libunistring5_1.3-1_amd64.deb ...
Unpacking libunistring5:amd64 (1.3-1) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../24-libicu72_72.1-6_amd64.deb ...
Unpacking libicu72:amd64 (72.1-6) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ...
Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.23.1-1_amd64.deb ...
Unpacking gettext (0.23.1-1) ...
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_13.24.1_all.deb ...
Unpacking debhelper (13.24.1) ...
Setting up libpipeline1:amd64 (1.5.8-1) ...
Setting up libicu72:amd64 (72.1-6) ...
Setting up bsdextrautils (2.40.4-3) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libmagic1t64:amd64 (1:5.45-3+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-5) ...
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:amd64 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libunistring5:amd64 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:amd64 (0.0.8-1+b2) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libtool (2.5.4-3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.40-7) ...
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: user script /srv/workspace/pbuilder/1611040/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/1611040/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/jellyfish1-1.1.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../jellyfish1_1.1.11-10_source.changes
dpkg-buildpackage: info: source package jellyfish1
dpkg-buildpackage: info: source version 1.1.11-10
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/build/reproducible-path/jellyfish1-1.1.11'
dh_clean
if [ -d debian/tmp_save_tests ] ; then \
mv debian/tmp_save_tests/* tests ; \
rmdir debian/tmp_save_tests ; \
fi
make[1]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11'
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac: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=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
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 xargs -n works... 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 x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for 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 ranlib... ranlib
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
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 -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for g++... g++
checking whether 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 -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for md5sum... md5sum
checking for __int128... yes
checking 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 -fcf-protection -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 -fcf-protection -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<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::simple_growing_array<char>::SimpleGrowingArrayError]':
./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array<T>::resize() [with T = char]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array<T>::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]'
27 | _capacity(capacity / 2), _size(0), _data(0) { resize(); }
| ^~~~~~
./jellyfish/seq_qual_parser.hpp:53:41: required from here
53 | seq_qual_parser(fd, path, str, len) {}
| ^
./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<err_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<long unsigned int, atomic::gcc, allocators::mmap>; storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/raw_dumper.hpp:98:20: required from 'jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]'
98 | _ary = init(_file, hash_matrix, hash_inverse_matrix);
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
jellyfish/stats_main.cc:83:34: required from here
83 | raw_inv_hash_query_t hash(dbf);
| ^
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/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<word, atomic_t, mem_block_t>::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<long unsigned int, atomic::gcc, allocators::mmap>]' 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<long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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<word, atomic_t, mem_block_t>::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<long unsigned int, atomic::gcc, allocators::mmap>]' 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<long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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 -fcf-protection -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<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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/mer_counting.hpp:31,
from jellyfish/hash_merge.cc:34:
./jellyfish/compacted_hash.hpp: In instantiation of 'void jellyfish::compacted_hash::writer<storage_t>::write_header(std::ostream*) const [with storage_t = jellyfish::compacted_hash::reader<long unsigned int, long unsigned int>; std::ostream = std::basic_ostream<char>]':
jellyfish/hash_merge.cc:189:38: required from here
189 | info.buffers[0].writer.write_header(&out);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
./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<err_t>::~raise_t() [with err_t = jellyfish::simple_growing_array<char>::SimpleGrowingArrayError]':
./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array<T>::resize() [with T = char]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array<T>::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]'
27 | _capacity(capacity / 2), _size(0), _data(0) { resize(); }
| ^~~~~~
./jellyfish/seq_qual_parser.hpp:53:41: required from here
53 | seq_qual_parser(fd, path, str, len) {}
| ^
./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<key_t, val_t>::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<T> 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<key_t, val_t>::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<T> 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<key_t, val_t>::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<T> 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<key_t, val_t>::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<T> 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 -fcf-protection -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<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::invertible_hash::ErrorAllocation]':
./jellyfish/invertible_hash_array.hpp:116:11: required from 'jellyfish::invertible_hash::array<word, atomic_t, mem_block_t>::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]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
jellyfish/mer_counter.cc:142:66: required from here
142 | jellyfish::quadratic_reprobes);
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::invertible_hash::InvalidMatrix]':
./jellyfish/invertible_hash_array.hpp:185:11: required from 'void jellyfish::invertible_hash::array<word, atomic_t, mem_block_t>::set_matrix(SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
jellyfish/mer_counter.cc:149:22: required from here
149 | ary->set_matrix(m);
| ~~~~~~~~~~~~~~~^~~
./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<err_t>::~raise_t() [with err_t = jellyfish::simple_growing_array<char>::SimpleGrowingArrayError]':
./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array<T>::resize() [with T = char]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array<T>::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]'
27 | _capacity(capacity / 2), _size(0), _data(0) { resize(); }
| ^~~~~~
./jellyfish/seq_qual_parser.hpp:53:41: required from here
53 | seq_qual_parser(fd, path, str, len) {}
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::double_fifo_input<jellyfish::sequence_parser::sequence_t>::Error]':
./jellyfish/double_fifo_input.hpp:101:7: required from 'jellyfish::double_fifo_input<T>::double_fifo_input(long unsigned int) [with T = jellyfish::sequence_parser::sequence_t]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./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<const char* const*, std::vector<const char*> >; uint_t = long unsigned int; size_t = long unsigned int]'
178 | have_seam(false), buffer_data(buffer_size * nb_buffers), canonical(false)
| ^
jellyfish/mer_counter.cc:138:60: required from here
138 | args->buffer_size_arg);
| ^
./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/mer_counting.hpp:31,
from jellyfish/mer_counter.cc:38:
./jellyfish/compacted_hash.hpp: In instantiation of 'void jellyfish::compacted_hash::writer<storage_t>::write_header(std::ostream*) const [with storage_t = jellyfish::direct_indexing::array<long unsigned int, jellyfish::capped_integer<unsigned int>, atomic::gcc, allocators::mmap>; std::ostream = std::basic_ostream<char>]':
./jellyfish/direct_sorted_dumper.hpp:101:39: required from 'void jellyfish::direct_sorted_dumper<storage_t, atomic_t>::_dump() [with storage_t = jellyfish::direct_indexing::array<long unsigned int, jellyfish::capped_integer<unsigned int>, atomic::gcc, allocators::mmap>; atomic_t = atomic::gcc]'
101 | thread_info[0].writer.write_header(out);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
./jellyfish/direct_sorted_dumper.hpp:91:8: required from here
91 | void direct_sorted_dumper<storage_t,atomic_t>::_dump() {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./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<storage_t>::write_header(std::ostream*) const [with storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>; std::ostream = std::basic_ostream<char>]':
./jellyfish/sorted_dumper.hpp:116:39: required from 'void jellyfish::sorted_dumper<storage_t, atomic_t>::_dump() [with storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>; atomic_t = atomic::gcc]'
116 | thread_info[0].writer.write_header(out);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
./jellyfish/sorted_dumper.hpp:105:8: required from here
105 | void sorted_dumper<storage_t,atomic_t>::_dump() {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./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<err_t>::~raise_t() [with err_t = jellyfish::hash<long unsigned int, jellyfish::Float, jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>, atomic::gcc>::TableFull]':
./jellyfish/hash.hpp:151:9: required from 'void jellyfish::hash<key_t, val_t, ary_t, atomic>::dump() [with key_t = long unsigned int; val_t = jellyfish::Float; ary_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>; atomic = atomic::gcc]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
jellyfish/mer_counter.cc:114:17: required from 'void mer_counting<parser_t, hash_t>::start(int) [with parser_t = jellyfish::parse_quake; hash_t = jellyfish::hash<long unsigned int, jellyfish::Float, jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>, atomic::gcc>]'
114 | hash->dump();
| ~~~~~~~~~~^~
jellyfish/mer_counter.cc:97:8: required from here
97 | void start(int id) {
| ^~~~~
./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<err_t>::~raise_t() [with err_t = jellyfish::hash<long unsigned int, jellyfish::capped_integer<unsigned int>, jellyfish::direct_indexing::array<long unsigned int, jellyfish::capped_integer<unsigned int>, atomic::gcc, allocators::mmap>, atomic::gcc>::TableFull]':
./jellyfish/hash.hpp:151:9: required from 'void jellyfish::hash<key_t, val_t, ary_t, atomic>::dump() [with key_t = long unsigned int; val_t = jellyfish::capped_integer<unsigned int>; ary_t = jellyfish::direct_indexing::array<long unsigned int, jellyfish::capped_integer<unsigned int>, atomic::gcc, allocators::mmap>; atomic = atomic::gcc]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
jellyfish/mer_counter.cc:114:17: required from 'void mer_counting<parser_t, hash_t>::start(int) [with parser_t = jellyfish::parse_qual_dna; hash_t = jellyfish::hash<long unsigned int, jellyfish::capped_integer<unsigned int>, jellyfish::direct_indexing::array<long unsigned int, jellyfish::capped_integer<unsigned int>, atomic::gcc, allocators::mmap>, atomic::gcc>]'
114 | hash->dump();
| ~~~~~~~~~~^~
jellyfish/mer_counter.cc:97:8: required from here
97 | void start(int id) {
| ^~~~~
./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<err_t>::~raise_t() [with err_t = jellyfish::hash<long unsigned int, long unsigned int, jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>, atomic::gcc>::TableFull]':
./jellyfish/hash.hpp:151:9: required from 'void jellyfish::hash<key_t, val_t, ary_t, atomic>::dump() [with key_t = long unsigned int; val_t = long unsigned int; ary_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>; atomic = atomic::gcc]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
jellyfish/mer_counter.cc:114:17: required from 'void mer_counting<parser_t, hash_t>::start(int) [with parser_t = jellyfish::parse_qual_dna; hash_t = jellyfish::hash<long unsigned int, long unsigned int, jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>, atomic::gcc>]'
114 | hash->dump();
| ~~~~~~~~~~^~
jellyfish/mer_counter.cc:97:8: required from here
97 | void start(int id) {
| ^~~~~
./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(int)' at ./jellyfish/square_binary_matrix.hpp:61:62,
inlined from 'void jellyfish::direct_indexing::array<key_t, val_t, atomic_t, mem_block_t>::write_ary_header(std::ostream*) const [with key_t = long unsigned int; val_t = jellyfish::capped_integer<unsigned int>; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/direct_indexing_array.hpp:52:28,
inlined from 'void jellyfish::compacted_hash::writer<storage_t>::write_header(std::ostream*) const [with storage_t = jellyfish::direct_indexing::array<long unsigned int, jellyfish::capped_integer<unsigned int>, atomic::gcc, allocators::mmap>]' at ./jellyfish/compacted_hash.hpp:121:30,
inlined from 'void jellyfish::direct_sorted_dumper<storage_t, atomic_t>::_dump() [with storage_t = jellyfish::direct_indexing::array<long unsigned int, jellyfish::capped_integer<unsigned int>, 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<storage_t, atomic_t>::_dump() [with storage_t = jellyfish::direct_indexing::array<long unsigned int, jellyfish::capped_integer<unsigned int>, atomic::gcc, allocators::mmap>; atomic_t = atomic::gcc]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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<word, atomic_t, mem_block_t>::set_matrix(SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]' at ./jellyfish/invertible_hash_array.hpp:187:23,
inlined from 'void jellyfish::invertible_hash::array<word, atomic_t, mem_block_t>::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<word, atomic_t, mem_block_t>::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<T> 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<word, atomic_t, mem_block_t>::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<word, atomic_t, mem_block_t>::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<T> 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 -fcf-protection -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<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::simple_growing_array<char>::SimpleGrowingArrayError]':
./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array<T>::resize() [with T = char]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array<T>::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]'
27 | _capacity(capacity / 2), _size(0), _data(0) { resize(); }
| ^~~~~~
./jellyfish/seq_qual_parser.hpp:53:41: required from here
53 | seq_qual_parser(fd, path, str, len) {}
| ^
./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<err_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<long unsigned int, atomic::gcc, allocators::mmap>; storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/raw_dumper.hpp:98:20: required from 'jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]'
98 | _ary = init(_file, hash_matrix, hash_inverse_matrix);
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
jellyfish/histo_main.cc:111:34: required from here
111 | raw_inv_hash_query_t hash(dbf);
| ^
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/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<word, atomic_t, mem_block_t>::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<long unsigned int, atomic::gcc, allocators::mmap>]' 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<long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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<word, atomic_t, mem_block_t>::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<long unsigned int, atomic::gcc, allocators::mmap>]' 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<long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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<key_t, val_t>::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<T> 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<key_t, val_t>::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<T> 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 -fcf-protection -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<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::simple_growing_array<char>::SimpleGrowingArrayError]':
./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array<T>::resize() [with T = char]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array<T>::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]'
27 | _capacity(capacity / 2), _size(0), _data(0) { resize(); }
| ^~~~~~
./jellyfish/seq_qual_parser.hpp:53:41: required from here
53 | seq_qual_parser(fd, path, str, len) {}
| ^
./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<err_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<long unsigned int, atomic::gcc, allocators::mmap>; storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/raw_dumper.hpp:98:20: required from 'jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]'
98 | _ary = init(_file, hash_matrix, hash_inverse_matrix);
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
jellyfish/dump_main.cc:65:44: required from here
65 | raw_inv_hash_query_t hash(dbf);
| ^
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/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<word, atomic_t, mem_block_t>::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<long unsigned int, atomic::gcc, allocators::mmap>]' 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<long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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<word, atomic_t, mem_block_t>::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<long unsigned int, atomic::gcc, allocators::mmap>]' 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<long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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 -fcf-protection -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<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::simple_growing_array<char>::SimpleGrowingArrayError]':
./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array<T>::resize() [with T = char]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array<T>::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]'
27 | _capacity(capacity / 2), _size(0), _data(0) { resize(); }
| ^~~~~~
./jellyfish/seq_qual_parser.hpp:53:41: required from here
53 | seq_qual_parser(fd, path, str, len) {}
| ^
./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<err_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<long unsigned int, atomic::gcc, allocators::mmap>; storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/raw_dumper.hpp:98:20: required from 'jellyfish::raw_hash::query<_storage_t>::query(mapped_file&) [with _storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]'
98 | _ary = init(_file, hash_matrix, hash_inverse_matrix);
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
jellyfish/query_main.cc:63:34: required from here
63 | raw_inv_hash_query_t hash(dbf);
| ^
./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:
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<word, atomic_t, mem_block_t>::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<long unsigned int, atomic::gcc, allocators::mmap>]' 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<long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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<word, atomic_t, mem_block_t>::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<long unsigned int, atomic::gcc, allocators::mmap>]' 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<long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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 -fcf-protection -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<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::simple_growing_array<char>::SimpleGrowingArrayError]':
./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array<T>::resize() [with T = char]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array<T>::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]'
27 | _capacity(capacity / 2), _size(0), _data(0) { resize(); }
| ^~~~~~
./jellyfish/seq_qual_parser.hpp:53:41: required from here
53 | seq_qual_parser(fd, path, str, len) {}
| ^
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/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<word, atomic_t, mem_block_t>::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<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]' 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<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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<word, atomic_t, mem_block_t>::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<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]' 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<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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 -fcf-protection -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<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::simple_growing_array<char>::SimpleGrowingArrayError]':
./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array<T>::resize() [with T = char]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array<T>::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]'
27 | _capacity(capacity / 2), _size(0), _data(0) { resize(); }
| ^~~~~~
./jellyfish/seq_qual_parser.hpp:53:41: required from here
53 | seq_qual_parser(fd, path, str, len) {}
| ^
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/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<word, atomic_t, mem_block_t>::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<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]' 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<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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<word, atomic_t, mem_block_t>::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<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]' 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<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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 -fcf-protection -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 -fcf-protection -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<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::hash<long unsigned int, jellyfish::Float, jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>, atomic::gcc>::TableFull]':
./jellyfish/hash.hpp:151:9: required from 'void jellyfish::hash<key_t, val_t, ary_t, atomic>::dump() [with key_t = long unsigned int; val_t = jellyfish::Float; ary_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>; atomic = atomic::gcc]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
jellyfish/hash_fastq_merge.cc:49:12: required from here
49 | hash.dump();
| ~~~~~~~~~^~
./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<err_t>::~raise_t() [with err_t = jellyfish::simple_growing_array<char>::SimpleGrowingArrayError]':
./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array<T>::resize() [with T = char]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array<T>::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]'
27 | _capacity(capacity / 2), _size(0), _data(0) { resize(); }
| ^~~~~~
./jellyfish/seq_qual_parser.hpp:53:41: required from here
53 | seq_qual_parser(fd, path, str, len) {}
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::invertible_hash::ErrorAllocation]':
./jellyfish/invertible_hash_array.hpp:116:11: required from 'jellyfish::invertible_hash::array<word, atomic_t, mem_block_t>::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]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./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]'
41 | keys(_size, _key_len, 0, _reprobe_limit, _reprobes),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
jellyfish/hash_fastq_merge.cc:28:79: required from here
28 | args.reprobes_arg, jellyfish::quadratic_reprobes);
| ^
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/hash_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<word, atomic_t, mem_block_t>::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<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]' 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<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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<word, atomic_t, mem_block_t>::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<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]' 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<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]':
./jellyfish/misc.hpp:106:11: note: '*&ptr' was declared here
106 | Tptr<T> 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<word, atomic_t, mem_block_t>::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<word, atomic_t, mem_block_t>::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<T> 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 -fcf-protection -c -o jellyfish/yaggo.o jellyfish/yaggo.cpp
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::SingularMatrix]':
jellyfish/square_binary_matrix.cc:93:2: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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 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<T> 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<T> 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<T> 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<T> 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<T> 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<T> 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 -fcf-protection -c jellyfish/square_binary_matrix.cc -o jellyfish/square_binary_matrix.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c jellyfish/err.cc -o jellyfish/err.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c jellyfish/misc.cc -o jellyfish/misc.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c jellyfish/storage.cc -o jellyfish/storage.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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<err_t>::~raise_t() [with err_t = thread_exec::Error]':
jellyfish/thread_exec.cc:28:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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 -fcf-protection -c jellyfish/thread_exec.cc -o jellyfish/thread_exec.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c jellyfish/time.cc -o jellyfish/time.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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<err_t>::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]':
jellyfish/file_parser.cc:33:5: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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 -fcf-protection -c jellyfish/file_parser.cc -o jellyfish/file_parser.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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<err_t>::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]':
jellyfish/read_parser.cc:30:5: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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 -fcf-protection -c jellyfish/read_parser.cc -o jellyfish/read_parser.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c jellyfish/parse_read.cc -o jellyfish/parse_read.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c jellyfish/half.cpp -o jellyfish/half.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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 -fcf-protection -c jellyfish/mapped_file.cc -o jellyfish/mapped_file.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c jellyfish/parse_dna.cc -o jellyfish/parse_dna.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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<err_t>::~raise_t() [with err_t = jellyfish::double_fifo_input<jellyfish::seq_qual_parser::sequence_t>::Error]':
./jellyfish/double_fifo_input.hpp:101:7: required from 'jellyfish::double_fifo_input<T>::double_fifo_input(long unsigned int) [with T = jellyfish::seq_qual_parser::sequence_t]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
jellyfish/parse_quake.cc:27:40: required from here
27 | quality_start(_qs), canonical(false)
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::simple_growing_array<char>::SimpleGrowingArrayError]':
./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array<T>::resize() [with T = char]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array<T>::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]'
27 | _capacity(capacity / 2), _size(0), _data(0) { resize(); }
| ^~~~~~
./jellyfish/seq_qual_parser.hpp:53:41: required from here
53 | seq_qual_parser(fd, path, str, len) {}
| ^
./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 -fcf-protection -c jellyfish/parse_quake.cc -o jellyfish/parse_quake.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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<err_t>::~raise_t() [with err_t = jellyfish::double_fifo_input<jellyfish::seq_qual_parser::sequence_t>::Error]':
./jellyfish/double_fifo_input.hpp:101:7: required from 'jellyfish::double_fifo_input<T>::double_fifo_input(long unsigned int) [with T = jellyfish::seq_qual_parser::sequence_t]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
jellyfish/parse_qual_dna.cc:27:55: required from here
27 | quality_start(_qs), min_q(_min_q), canonical(false)
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::simple_growing_array<char>::SimpleGrowingArrayError]':
./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array<T>::resize() [with T = char]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array<T>::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]'
27 | _capacity(capacity / 2), _size(0), _data(0) { resize(); }
| ^~~~~~
./jellyfish/seq_qual_parser.hpp:53:41: required from here
53 | seq_qual_parser(fd, path, str, len) {}
| ^
./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 -fcf-protection -c jellyfish/parse_qual_dna.cc -o jellyfish/parse_qual_dna.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -c jellyfish/sequence_parser.cc -fPIC -DPIC -o jellyfish/.libs/sequence_parser.o
In file included from ./jellyfish/sequence_parser.hpp:21,
from jellyfish/sequence_parser.cc:18:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]':
jellyfish/sequence_parser.cc:32:5: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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 -fcf-protection -c jellyfish/sequence_parser.cc -o jellyfish/sequence_parser.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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<err_t>::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]':
jellyfish/seq_qual_parser.cc:31:5: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::fastq_seq_qual_parser::FastqSeqQualParserError]':
jellyfish/seq_qual_parser.cc:47:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = jellyfish::simple_growing_array<char>::SimpleGrowingArrayError]':
./jellyfish/simple_growing_array.hpp:55:9: required from 'void jellyfish::simple_growing_array<T>::resize() [with T = char]'
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^~~~~~~~~~~~
./jellyfish/simple_growing_array.hpp:27:53: required from 'jellyfish::simple_growing_array<T>::simple_growing_array(size_t) [with T = char; size_t = long unsigned int]'
27 | _capacity(capacity / 2), _size(0), _data(0) { resize(); }
| ^~~~~~
./jellyfish/seq_qual_parser.hpp:53:41: required from here
53 | seq_qual_parser(fd, path, str, len) {}
| ^
./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 -fcf-protection -c jellyfish/seq_qual_parser.cc -o jellyfish/seq_qual_parser.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c jellyfish/backtrace.cc -o jellyfish/backtrace.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c jellyfish/floats.cc -o jellyfish/floats.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c jellyfish/dbg.cc -o jellyfish/dbg.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c jellyfish/allocators_mmap.cc -o jellyfish/allocators_mmap.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c jellyfish/dna_codes.cc -o jellyfish/dna_codes.o >/dev/null 2>&1
/bin/sh ./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 -fcf-protection -version-info 1:1:0 -Wl,-z,relro -Wl,-z,now -o libjellyfish-1.1.la -rpath /usr/lib/x86_64-linux-gnu jellyfish/square_binary_matrix.lo jellyfish/err.lo jellyfish/misc.lo jellyfish/storage.lo jellyfish/thread_exec.lo jellyfish/time.lo jellyfish/file_parser.lo jellyfish/read_parser.lo jellyfish/parse_read.lo jellyfish/half.lo jellyfish/mapped_file.lo jellyfish/parse_dna.lo jellyfish/parse_quake.lo jellyfish/parse_qual_dna.lo jellyfish/sequence_parser.lo jellyfish/seq_qual_parser.lo jellyfish/backtrace.lo jellyfish/floats.lo jellyfish/dbg.lo jellyfish/allocators_mmap.lo jellyfish/dna_codes.lo
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o jellyfish/.libs/square_binary_matrix.o jellyfish/.libs/err.o jellyfish/.libs/misc.o jellyfish/.libs/storage.o jellyfish/.libs/thread_exec.o jellyfish/.libs/time.o jellyfish/.libs/file_parser.o jellyfish/.libs/read_parser.o jellyfish/.libs/parse_read.o jellyfish/.libs/half.o jellyfish/.libs/mapped_file.o jellyfish/.libs/parse_dna.o jellyfish/.libs/parse_quake.o jellyfish/.libs/parse_qual_dna.o jellyfish/.libs/sequence_parser.o jellyfish/.libs/seq_qual_parser.o jellyfish/.libs/backtrace.o jellyfish/.libs/floats.o jellyfish/.libs/dbg.o jellyfish/.libs/allocators_mmap.o jellyfish/.libs/dna_codes.o -L/usr/lib/gcc/x86_64-linux-gnu/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o -g -O3 -g -O2 -ffile-prefix-map=/build/reproducible-path/jellyfish1-1.1.11=. -fstack-protector-strong -Werror=format-security -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/sh ./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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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/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<T> 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<T> 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:80:50:
./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<T> 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 -fcf-protection -c -o jellyfish/mersenne.o jellyfish/mersenne.cpp
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
139 | #define eraise(e) if(1) err::raise_t<e>()
| ^
./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 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<T> 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<T> 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<T> 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<T> 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<T> 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<T> 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<T> 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 -fcf-protection -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 -fcf-protection -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 cr libgtest.a unit_tests/gtest/src/libgtest_a-gtest-all.o
ranlib libgtest.a
rm -f libgtest_main.a
ar cr libgtest_main.a unit_tests/gtest/src/libgtest_main_a-gtest_main.o libgtest.a
ranlib libgtest_main.a
/bin/sh ./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 -fcf-protection -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 -fcf-protection -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/x86_64-linux-gnu'
/bin/sh ./libtool --mode=install /usr/bin/install -c libjellyfish-1.1.la '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu'
libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.so.1.0.1 /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.so.1.0.1
libtool: install: (cd /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so.1 || { rm -f libjellyfish-1.1.so.1 && ln -s libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so.1; }; })
libtool: install: (cd /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so || { rm -f libjellyfish-1.1.so && ln -s libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so; }; })
libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.lai /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.a /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.a
libtool: install: chmod 644 /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.a
libtool: install: ranlib /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-1.1.a
libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu'
/usr/bin/mkdir -p '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/bin'
/bin/sh ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/bin'
libtool: warning: 'libjellyfish-1.1.la' has not been installed in '/usr/lib/x86_64-linux-gnu'
libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/bin/jellyfish
/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/x86_64-linux-gnu/pkgconfig'
/usr/bin/install -c -m 644 jellyfish-1.1.pc '/build/reproducible-path/jellyfish1-1.1.11/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig'
make[3]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11'
make[2]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11'
make[1]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/jellyfish1-1.1.11'
mkdir -p debian/tmp/usr/lib/jellyfish1
mv debian/tmp/usr/bin/* debian/tmp/usr/lib/jellyfish1
dh_install
find debian -name "*.a" -delete
find debian -name "*.la" -delete
find debian -name "*.so" -delete
find debian -name "pkgconfig" -type d | xargs rm -rf
# there is no development package for this version any more - remove header files to keep dh_missing happy
rm -rf debian/tmp/usr/include/jellyfish*
make[1]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11'
dh_installdocs
dh_installchangelogs
debian/rules override_dh_installman
make[1]: Entering directory '/build/reproducible-path/jellyfish1-1.1.11'
dh_installman
mv debian/jellyfish1/usr/share/man/man1/jellyfish.1 debian/jellyfish1/usr/share/man/man1/jellyfish1.1
make[1]: Leaving directory '/build/reproducible-path/jellyfish1-1.1.11'
dh_lintian
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'jellyfish1-dbgsym' in '../jellyfish1-dbgsym_1.1.11-10_amd64.deb'.
dpkg-deb: building package 'jellyfish1' in '../jellyfish1_1.1.11-10_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../jellyfish1_1.1.11-10_amd64.buildinfo
dpkg-genchanges --build=binary -O../jellyfish1_1.1.11-10_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/1611040/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/1611040/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/1611040 and its subdirectories
I: Current time: Tue Feb 18 01:42:19 +14 2025
I: pbuilder-time-stamp: 1739792539