Tue Jul 13 12:25:46 UTC 2021 I: starting to build jellyfish1/bullseye/arm64 on jenkins on '2021-07-13 12:25'
Tue Jul 13 12:25:46 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_21/30950/console.log
Tue Jul 13 12:25:46 UTC 2021 I: Downloading source for bullseye/jellyfish1=1.1.11-5
--2021-07-13 12:25:46-- http://cdn-fastly.deb.debian.org/debian/pool/main/j/jellyfish1/jellyfish1_1.1.11-5.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2015 (2.0K)
Saving to: ‘jellyfish1_1.1.11-5.dsc’
0K . 100% 310M=0s
2021-07-13 12:25:46 (310 MB/s) - ‘jellyfish1_1.1.11-5.dsc’ saved [2015/2015]
Tue Jul 13 12:25:46 UTC 2021 I: jellyfish1_1.1.11-5.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: jellyfish1
Binary: jellyfish1
Architecture: any
Version: 1.1.11-5
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Shaun Jackman <sjackman@debian.org>, Andreas Tille <tille@debian.org>
Homepage: https://www.cbcb.umd.edu/software/jellyfish/
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/jellyfish1
Vcs-Git: https://salsa.debian.org/med-team/jellyfish1.git
Build-Depends: debhelper-compat (= 13)
Package-List:
jellyfish1 deb science optional arch=any
Checksums-Sha1:
8bd6a7b382e94d37adfddd916dec2b0e36f840fd 1067138 jellyfish1_1.1.11.orig.tar.gz
a0d7aa2ce53dfef055a55bbedcc302ea166460e7 5016 jellyfish1_1.1.11-5.debian.tar.xz
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496645d96b08ba35db1f856d857a159798c73cbc1eccb852ef1b253d1678c8e2 1067138 jellyfish1_1.1.11.orig.tar.gz
37eae87742011610c68078ac1fda923bedcba924fca4161969493f8ca84819da 5016 jellyfish1_1.1.11-5.debian.tar.xz
Files:
dc994ea8b0896156500ea8c648f24846 1067138 jellyfish1_1.1.11.orig.tar.gz
d49be598ea2ed67eedb246e5db1878cb 5016 jellyfish1_1.1.11-5.debian.tar.xz
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Tue Jul 13 12:25:46 UTC 2021 I: Checking whether the package is not for us
Tue Jul 13 12:25:46 UTC 2021 I: Starting 1st build on remote node codethink14-arm64.debian.net.
Tue Jul 13 12:25:46 UTC 2021 I: Preparing to do remote build '1' on codethink14-arm64.debian.net.
Tue Jul 13 12:29:59 UTC 2021 I: Deleting $TMPDIR on codethink14-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Tue Jul 13 00:25:49 -12 2021
I: pbuilder-time-stamp: 1626179149
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz]
I: copying local configuration
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [jellyfish1_1.1.11-5.dsc]
I: copying [./jellyfish1_1.1.11.orig.tar.gz]
I: copying [./jellyfish1_1.1.11-5.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.W5Pbpj6T/trustedkeys.kbx': General error
gpgv: Signature made Wed Nov 25 19:14:01 2020 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./jellyfish1_1.1.11-5.dsc
dpkg-source: info: extracting jellyfish1 in jellyfish1-1.1.11
dpkg-source: info: unpacking jellyfish1_1.1.11.orig.tar.gz
dpkg-source: info: unpacking jellyfish1_1.1.11-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying man
dpkg-source: info: applying arm64.patch
dpkg-source: info: applying mips.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/30987/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8'
DISTRIBUTION=''
HOME='/var/lib/jenkins'
HOST_ARCH='arm64'
IFS='
'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='30987'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.E2nu0kmgZb/pbuilderrc_GmPS --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.E2nu0kmgZb/b1 --logfile b1/build.log jellyfish1_1.1.11-5.dsc'
SUDO_GID='117'
SUDO_UID='110'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
USERNAME='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.16:3128'
I: uname -a
Linux codethink14-arm64 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux
I: ls -l /bin
total 5252
-rwxr-xr-x 1 root root 1282512 Jun 21 14:26 bash
-rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2
-rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep
-rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2
-rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore
-rwxr-xr-x 1 root root 39832 Sep 22 2020 cat
-rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp
-rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod
-rwxr-xr-x 1 root root 64528 Sep 22 2020 chown
-rwxr-xr-x 1 root root 138896 Sep 22 2020 cp
-rwxr-xr-x 1 root root 129544 Dec 10 2020 dash
-rwxr-xr-x 1 root root 101384 Sep 22 2020 date
-rwxr-xr-x 1 root root 80984 Sep 22 2020 dd
-rwxr-xr-x 1 root root 89824 Sep 22 2020 df
-rwxr-xr-x 1 root root 143088 Sep 22 2020 dir
-rwxr-xr-x 1 root root 76152 Feb 7 02:38 dmesg
lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname
-rwxr-xr-x 1 root root 35632 Sep 22 2020 echo
-rwxr-xr-x 1 root root 28 Nov 9 2020 egrep
-rwxr-xr-x 1 root root 31512 Sep 22 2020 false
-rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep
-rwxr-xr-x 1 root root 64856 Feb 7 02:38 findmnt
-rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount
-rwxr-xr-x 1 root root 178400 Nov 9 2020 grep
-rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip
-rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe
-rwxr-xr-x 1 root root 93744 Mar 2 11:30 gzip
-rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname
-rwxr-xr-x 1 root root 68720 Sep 22 2020 ln
-rwxr-xr-x 1 root root 52720 Feb 7 2020 login
-rwxr-xr-x 1 root root 143088 Sep 22 2020 ls
-rwxr-xr-x 1 root root 161960 Feb 7 02:38 lsblk
-rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir
-rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod
-rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp
-rwxr-xr-x 1 root root 51368 Feb 7 02:38 more
-rwsr-xr-x 1 root root 51360 Feb 7 02:38 mount
-rwxr-xr-x 1 root root 14496 Feb 7 02:38 mountpoint
-rwxr-xr-x 1 root root 134808 Sep 22 2020 mv
lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd
lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash
-rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink
-rwxr-xr-x 1 root root 68592 Sep 22 2020 rm
-rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir
-rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts
-rwxr-xr-x 1 root root 114016 Dec 22 2018 sed
lrwxrwxrwx 1 root root 4 Jul 11 21:26 sh -> dash
-rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep
-rwxr-xr-x 1 root root 72640 Sep 22 2020 stty
-rwsr-xr-x 1 root root 67776 Feb 7 02:38 su
-rwxr-xr-x 1 root root 35672 Sep 22 2020 sync
-rwxr-xr-x 1 root root 535768 Feb 16 21:55 tar
-rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile
-rwxr-xr-x 1 root root 89120 Sep 22 2020 touch
-rwxr-xr-x 1 root root 31512 Sep 22 2020 true
-rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server
-rwsr-xr-x 1 root root 30880 Feb 7 02:38 umount
-rwxr-xr-x 1 root root 35640 Sep 22 2020 uname
-rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress
-rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir
-rwxr-xr-x 1 root root 59584 Feb 7 02:38 wdctl
lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat
-rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp
-rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff
-rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep
-rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep
-rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce
-rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep
-rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless
-rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore
-rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew
I: user script /srv/workspace/pbuilder/30987/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <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 ... 19646 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 31 newly installed, 0 to remove and 0 not upgraded.
Need to get 17.9 MB of archives. After unpacking 67.3 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB]
Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB]
Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB]
Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB]
Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB]
Get: 6 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB]
Get: 7 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB]
Get: 8 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB]
Get: 9 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB]
Get: 10 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB]
Get: 11 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB]
Get: 12 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB]
Get: 13 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB]
Get: 14 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get: 15 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB]
Get: 16 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB]
Get: 17 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB]
Get: 18 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB]
Get: 19 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB]
Get: 22 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB]
Get: 23 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB]
Get: 24 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB]
Get: 25 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB]
Get: 26 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB]
Get: 27 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB]
Get: 28 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB]
Get: 29 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 30 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB]
Fetched 17.9 MB in 0s (41.7 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package bsdextrautils.
(Reading database ...
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19646 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.36.1-7_arm64.deb ...
Unpacking bsdextrautils (2.36.1-7) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ...
Unpacking groff-base (1.22.4-6) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.9.4-2_arm64.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ...
Unpacking sensible-utils (0.0.14) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_arm64.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:arm64.
Preparing to unpack .../07-libmagic1_1%3a5.39-3_arm64.deb ...
Unpacking libmagic1:arm64 (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../08-file_1%3a5.39-3_arm64.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../09-gettext-base_0.21-4_arm64.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package libsigsegv2:arm64.
Preparing to unpack .../10-libsigsegv2_2.13-1_arm64.deb ...
Unpacking libsigsegv2:arm64 (2.13-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../11-m4_1.4.18-5_arm64.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../12-autoconf_2.69-14_all.deb ...
Unpacking autoconf (2.69-14) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ...
Unpacking automake (1:1.16.3-2) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../15-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ...
Unpacking libdebhelper-perl (13.3.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/jellyfish1-1.1.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../jellyfish1_1.1.11-5_source.changes
dpkg-buildpackage: info: source package jellyfish1
dpkg-buildpackage: info: source version 1.1.11-5
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/build/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/jellyfish1-1.1.11'
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:9: installing './compile'
configure.ac:4: installing './missing'
Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/jellyfish1-1.1.11'
dh_auto_configure
./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking build system type... aarch64-unknown-linux-gnu
checking host system type... aarch64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for md5sum... md5sum
checking for __int128... yes
checking whether strerror_r is declared... yes
checking for strerror_r... yes
checking whether strerror_r returns char *... yes
checking execinfo.h usability... yes
checking execinfo.h presence... yes
checking for execinfo.h... yes
checking sys/syscall.h usability... yes
checking sys/syscall.h presence... yes
checking for sys/syscall.h... yes
checking for siginfo_t.si_int... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating tests/compat.sh
config.status: creating jellyfish-1.1.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
make[1]: Leaving directory '/build/jellyfish1-1.1.11'
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/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/jellyfish1-1.1.11'
make all-am
make[3]: Entering directory '/build/jellyfish1-1.1.11'
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/jellyfish.o jellyfish/jellyfish.cc
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/stats_main.o jellyfish/stats_main.cc
In file included from jellyfish/stats_main.cc:24:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
./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]'
./jellyfish/seq_qual_parser.hpp:53:41: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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>; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]'
./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>]'
jellyfish/stats_main.cc:83:34: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/stats_main.cc:26:
./jellyfish/square_binary_matrix.hpp: In static member function 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/stats_main.cc:25:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/stats_main.cc:26:
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/stats_main.cc:25:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/hash_merge.o jellyfish/hash_merge.cc
In file included from jellyfish/hash_merge.cc:32:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/mer_counting.hpp:31,
from jellyfish/hash_merge.cc:34:
./jellyfish/compacted_hash.hpp: In instantiation of 'void jellyfish::compacted_hash::writer<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:189:43: required from here
./jellyfish/compacted_hash.hpp:114:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct jellyfish::compacted_hash::header'; use assignment or value-initialization instead [-Wclass-memaccess]
114 | memset(&head, '\0', sizeof(head));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./jellyfish/compacted_hash.hpp:36:12: note: 'struct jellyfish::compacted_hash::header' declared here
36 | struct header {
| ^~~~~~
In file included from jellyfish/hash_merge.cc:32:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
./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]'
./jellyfish/seq_qual_parser.hpp:53:41: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/hash_merge.cc:34:
./jellyfish/square_binary_matrix.hpp: In function 'int merge_main(int, char**)':
./jellyfish/square_binary_matrix.hpp:87:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
87 | free(columns);
| ~~~~^~~~~~~~~
In file included from jellyfish/hash_merge.cc:33:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/hash_merge.cc:34:
./jellyfish/square_binary_matrix.hpp:87:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
87 | free(columns);
| ~~~~^~~~~~~~~
In file included from jellyfish/hash_merge.cc:33:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/hash_merge.cc:34:
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/hash_merge.cc:33:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/hash_merge.cc:34:
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/hash_merge.cc:33:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mer_counter.o jellyfish/mer_counter.cc
In file included from jellyfish/mer_counter.cc:33:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
jellyfish/mer_counter.cc:142:66: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
jellyfish/mer_counter.cc:149:24: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
./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]'
./jellyfish/seq_qual_parser.hpp:53:41: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
./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]'
jellyfish/mer_counter.cc:138:60: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/mer_counting.hpp:31,
from jellyfish/mer_counter.cc:38:
./jellyfish/compacted_hash.hpp: In instantiation of 'void jellyfish::compacted_hash::writer<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]'
./jellyfish/direct_sorted_dumper.hpp:91:8: required from here
./jellyfish/compacted_hash.hpp:114:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct jellyfish::compacted_hash::header'; use assignment or value-initialization instead [-Wclass-memaccess]
114 | memset(&head, '\0', sizeof(head));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./jellyfish/compacted_hash.hpp:36:12: note: 'struct jellyfish::compacted_hash::header' declared here
36 | struct header {
| ^~~~~~
./jellyfish/compacted_hash.hpp: In instantiation of 'void jellyfish::compacted_hash::writer<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]'
./jellyfish/sorted_dumper.hpp:105:8: required from here
./jellyfish/compacted_hash.hpp:114:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct jellyfish::compacted_hash::header'; use assignment or value-initialization instead [-Wclass-memaccess]
114 | memset(&head, '\0', sizeof(head));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./jellyfish/compacted_hash.hpp:36:12: note: 'struct jellyfish::compacted_hash::header' declared here
36 | struct header {
| ^~~~~~
In file included from jellyfish/mer_counter.cc:33:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
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>]'
jellyfish/mer_counter.cc:97:8: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
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>]'
jellyfish/mer_counter.cc:97:8: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
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>]'
jellyfish/mer_counter.cc:97:8: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from jellyfish/mer_counter.cc:36:
./jellyfish/misc.hpp: In member function 'void jellyfish::direct_sorted_dumper<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: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | Tptr<T> ptr;
| ^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/mer_counter.cc:38:
./jellyfish/square_binary_matrix.hpp: In member function 'void jellyfish::invertible_hash::array<word, atomic_t, mem_block_t>::set_matrix(SquareBinaryMatrix&) [with word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]':
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/mer_counter.cc:36:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/histo_main.o jellyfish/histo_main.cc
In file included from jellyfish/histo_main.cc:25:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
./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]'
./jellyfish/seq_qual_parser.hpp:53:41: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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>; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]'
./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>]'
jellyfish/histo_main.cc:111:34: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/histo_main.cc:27:
./jellyfish/square_binary_matrix.hpp: In static member function 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/histo_main.cc:26:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/histo_main.cc:27:
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/histo_main.cc:26:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/histo_main.cc:27:
./jellyfish/square_binary_matrix.hpp: In function 'int histo_main(int, char**)':
./jellyfish/square_binary_matrix.hpp:87:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
87 | free(columns);
| ~~~~^~~~~~~~~
In file included from jellyfish/histo_main.cc:26:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/histo_main.cc:27:
./jellyfish/square_binary_matrix.hpp:87:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
87 | free(columns);
| ~~~~^~~~~~~~~
In file included from jellyfish/histo_main.cc:26:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dump_main.o jellyfish/dump_main.cc
jellyfish/dump_main.cc: In function 'int dump_main(int, char**)':
jellyfish/dump_main.cc:86:24: warning: catching polymorphic type 'class mapped_file::ErrorMMap' by value [-Wcatch-value=]
86 | } catch(mapped_file::ErrorMMap) {
| ^~~~~~~~~
In file included from jellyfish/dump_main.cc:24:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
./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]'
./jellyfish/seq_qual_parser.hpp:53:41: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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>; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]'
./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>]'
jellyfish/dump_main.cc:65:44: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/dump_main.cc:26:
./jellyfish/square_binary_matrix.hpp: In static member function 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/dump_main.cc:25:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/dump_main.cc:26:
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/dump_main.cc:25:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/query_main.o jellyfish/query_main.cc
In file included from ./jellyfish/mapped_file.hpp:29,
from ./jellyfish/hash.hpp:27,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/query_main.cc:24:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
./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]'
./jellyfish/seq_qual_parser.hpp:53:41: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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>; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]'
./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>]'
jellyfish/query_main.cc:63:34: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/query_main.cc:24:
./jellyfish/square_binary_matrix.hpp: In static member function 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array<long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/query_main.cc:23:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/query_main.cc:24:
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/query_main.cc:23:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dump_fastq_main.o jellyfish/dump_fastq_main.cc
In file included from jellyfish/dump_fastq_main.cc:25:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
./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]'
./jellyfish/seq_qual_parser.hpp:53:41: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/dump_fastq_main.cc:27:
./jellyfish/square_binary_matrix.hpp: In static member function 'static storage_t* jellyfish::fastq_hash::raw_dumper<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]':
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/dump_fastq_main.cc:26:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/dump_fastq_main.cc:27:
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/dump_fastq_main.cc:26:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/histo_fastq_main.o jellyfish/histo_fastq_main.cc
In file included from jellyfish/histo_fastq_main.cc:26:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
./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]'
./jellyfish/seq_qual_parser.hpp:53:41: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/histo_fastq_main.cc:28:
./jellyfish/square_binary_matrix.hpp: In static member function 'static storage_t* jellyfish::fastq_hash::raw_dumper<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]':
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/histo_fastq_main.cc:27:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/histo_fastq_main.cc:28:
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/histo_fastq_main.cc:27:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/cite.o jellyfish/cite.cc
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/hash_fastq_merge.o jellyfish/hash_fastq_merge.cc
In file included from jellyfish/hash_fastq_merge.cc:17:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::dumper_t::ErrorWriting]':
./jellyfish/dumper.hpp:44:9: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::compacted_hash::ErrorReading]':
./jellyfish/compacted_hash.hpp:50:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::fastq_hash::ErrorReading]':
./jellyfish/fastq_dumper.hpp:46:11: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
jellyfish/hash_fastq_merge.cc:49:13: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
./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]'
./jellyfish/seq_qual_parser.hpp:53:41: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
./jellyfish/aligned_values_array.hpp:42:30: required from 'jellyfish::aligned_values::array<_key_t, _val_t, atomic, mem_block_t>::array(size_t, uint_t, uint_t, size_t*) [with _key_t = long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap; size_t = long unsigned int; uint_t = long unsigned int]'
jellyfish/hash_fastq_merge.cc:28:79: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/hash_fastq_merge.cc:19:
./jellyfish/square_binary_matrix.hpp: In static member function 'static storage_t* jellyfish::fastq_hash::raw_dumper<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]':
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/hash_fastq_merge.cc:18:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/hash_fastq_merge.cc:19:
./jellyfish/square_binary_matrix.hpp:69:18: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
69 | columns[i] = rhs.columns[i] & _mask;
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from jellyfish/hash_fastq_merge.cc:18:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/yaggo.o jellyfish/yaggo.cpp
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/square_binary_matrix.lo jellyfish/square_binary_matrix.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/square_binary_matrix.cc -fPIC -DPIC -o jellyfish/.libs/square_binary_matrix.o
In file included from ./jellyfish/square_binary_matrix.hpp:27,
from jellyfish/square_binary_matrix.cc:21:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::SingularMatrix]':
jellyfish/square_binary_matrix.cc:93:2: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from jellyfish/square_binary_matrix.cc:21:
./jellyfish/square_binary_matrix.hpp: In function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)':
./jellyfish/square_binary_matrix.hpp:46:12: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
46 | return res;
| ^~~
./jellyfish/square_binary_matrix.hpp: In member function 'void SquareBinaryMatrix::alloc_columns()':
./jellyfish/square_binary_matrix.hpp:55:13: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
55 | columns = first_alloc(size);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from jellyfish/square_binary_matrix.cc:20:
./jellyfish/misc.hpp: In member function 'SquareBinaryMatrix SquareBinaryMatrix::inverse() const':
./jellyfish/misc.hpp:106:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | Tptr<T> ptr;
| ^~~
jellyfish/square_binary_matrix.cc:110:19: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
110 | pivot.columns[j] ^= pivot.columns[i];
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/square_binary_matrix.cc -o jellyfish/square_binary_matrix.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/err.lo jellyfish/err.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/err.cc -fPIC -DPIC -o jellyfish/.libs/err.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/err.cc -o jellyfish/err.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/misc.lo jellyfish/misc.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/misc.cc -fPIC -DPIC -o jellyfish/.libs/misc.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/misc.cc -o jellyfish/misc.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/storage.lo jellyfish/storage.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/storage.cc -fPIC -DPIC -o jellyfish/.libs/storage.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/storage.cc -o jellyfish/storage.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/thread_exec.lo jellyfish/thread_exec.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/thread_exec.cc -fPIC -DPIC -o jellyfish/.libs/thread_exec.o
In file included from jellyfish/thread_exec.hpp:26,
from jellyfish/thread_exec.cc:17:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = thread_exec::Error]':
jellyfish/thread_exec.cc:28:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/thread_exec.cc -o jellyfish/thread_exec.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/time.lo jellyfish/time.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/time.cc -fPIC -DPIC -o jellyfish/.libs/time.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/time.cc -o jellyfish/time.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/file_parser.lo jellyfish/file_parser.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/file_parser.cc -fPIC -DPIC -o jellyfish/.libs/file_parser.o
In file included from jellyfish/file_parser.cc:17:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]':
jellyfish/file_parser.cc:33:5: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/file_parser.cc -o jellyfish/file_parser.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/read_parser.lo jellyfish/read_parser.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/read_parser.cc -fPIC -DPIC -o jellyfish/.libs/read_parser.o
In file included from ./jellyfish/file_parser.hpp:24,
from ./jellyfish/read_parser.hpp:20,
from jellyfish/read_parser.cc:17:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]':
jellyfish/read_parser.cc:30:5: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/read_parser.cc -o jellyfish/read_parser.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_read.lo jellyfish/parse_read.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_read.cc -fPIC -DPIC -o jellyfish/.libs/parse_read.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_read.cc -o jellyfish/parse_read.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/half.lo jellyfish/half.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/half.cpp -fPIC -DPIC -o jellyfish/.libs/half.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/half.cpp -o jellyfish/half.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mapped_file.lo jellyfish/mapped_file.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/mapped_file.cc -fPIC -DPIC -o jellyfish/.libs/mapped_file.o
In file included from ./jellyfish/mapped_file.hpp:29,
from jellyfish/mapped_file.cc:17:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/mapped_file.cc -o jellyfish/mapped_file.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_dna.lo jellyfish/parse_dna.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_dna.cc -fPIC -DPIC -o jellyfish/.libs/parse_dna.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_dna.cc -o jellyfish/parse_dna.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_quake.lo jellyfish/parse_quake.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_quake.cc -fPIC -DPIC -o jellyfish/.libs/parse_quake.o
In file included from ./jellyfish/double_fifo_input.hpp:23,
from ./jellyfish/parse_quake.hpp:22,
from jellyfish/parse_quake.cc:17:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
jellyfish/parse_quake.cc:27:40: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
./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]'
./jellyfish/seq_qual_parser.hpp:53:41: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_quake.cc -o jellyfish/parse_quake.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/parse_qual_dna.lo jellyfish/parse_qual_dna.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_qual_dna.cc -fPIC -DPIC -o jellyfish/.libs/parse_qual_dna.o
In file included from ./jellyfish/double_fifo_input.hpp:23,
from ./jellyfish/parse_qual_dna.hpp:22,
from jellyfish/parse_qual_dna.cc:17:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
jellyfish/parse_qual_dna.cc:27:55: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
./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]'
./jellyfish/seq_qual_parser.hpp:53:41: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/parse_qual_dna.cc -o jellyfish/parse_qual_dna.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/sequence_parser.lo jellyfish/sequence_parser.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/sequence_parser.cc -fPIC -DPIC -o jellyfish/.libs/sequence_parser.o
jellyfish/sequence_parser.cc: In member function 'virtual bool jellyfish::fasta_sequence_parser::parse(char*, char**)':
jellyfish/sequence_parser.cc:43:5: warning: case label value is less than minimum value for type [-Wswitch-outside-range]
43 | case _eof:
| ^~~~
In file included from ./jellyfish/sequence_parser.hpp:21,
from jellyfish/sequence_parser.cc:18:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]':
jellyfish/sequence_parser.cc:32:5: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/sequence_parser.cc -o jellyfish/sequence_parser.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/seq_qual_parser.lo jellyfish/seq_qual_parser.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/seq_qual_parser.cc -fPIC -DPIC -o jellyfish/.libs/seq_qual_parser.o
In file included from ./jellyfish/seq_qual_parser.hpp:21,
from jellyfish/seq_qual_parser.cc:17:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::file_parser::FileParserError]':
jellyfish/seq_qual_parser.cc:31:5: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = jellyfish::fastq_seq_qual_parser::FastqSeqQualParserError]':
jellyfish/seq_qual_parser.cc:47:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<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]'
./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]'
./jellyfish/seq_qual_parser.hpp:53:41: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/seq_qual_parser.cc -o jellyfish/seq_qual_parser.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/backtrace.lo jellyfish/backtrace.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/backtrace.cc -fPIC -DPIC -o jellyfish/.libs/backtrace.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/backtrace.cc -o jellyfish/backtrace.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/floats.lo jellyfish/floats.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/floats.cc -fPIC -DPIC -o jellyfish/.libs/floats.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/floats.cc -o jellyfish/floats.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dbg.lo jellyfish/dbg.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dbg.cc -fPIC -DPIC -o jellyfish/.libs/dbg.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dbg.cc -o jellyfish/dbg.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/allocators_mmap.lo jellyfish/allocators_mmap.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/allocators_mmap.cc -fPIC -DPIC -o jellyfish/.libs/allocators_mmap.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/allocators_mmap.cc -o jellyfish/allocators_mmap.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dna_codes.lo jellyfish/dna_codes.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dna_codes.cc -fPIC -DPIC -o jellyfish/.libs/dna_codes.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c jellyfish/dna_codes.cc -o jellyfish/dna_codes.o >/dev/null 2>&1
/bin/bash ./libtool --tag=CXX --mode=link g++ -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:1:0 -Wl,-z,relro -Wl,-z,now -o libjellyfish-1.1.la -rpath /usr/lib/aarch64-linux-gnu jellyfish/square_binary_matrix.lo jellyfish/err.lo jellyfish/misc.lo jellyfish/storage.lo jellyfish/thread_exec.lo jellyfish/time.lo jellyfish/file_parser.lo jellyfish/read_parser.lo jellyfish/parse_read.lo jellyfish/half.lo jellyfish/mapped_file.lo jellyfish/parse_dna.lo jellyfish/parse_quake.lo jellyfish/parse_qual_dna.lo jellyfish/sequence_parser.lo jellyfish/seq_qual_parser.lo jellyfish/backtrace.lo jellyfish/floats.lo jellyfish/dbg.lo jellyfish/allocators_mmap.lo jellyfish/dna_codes.lo
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/10/crtbeginS.o jellyfish/.libs/square_binary_matrix.o jellyfish/.libs/err.o jellyfish/.libs/misc.o jellyfish/.libs/storage.o jellyfish/.libs/thread_exec.o jellyfish/.libs/time.o jellyfish/.libs/file_parser.o jellyfish/.libs/read_parser.o jellyfish/.libs/parse_read.o jellyfish/.libs/half.o jellyfish/.libs/mapped_file.o jellyfish/.libs/parse_dna.o jellyfish/.libs/parse_quake.o jellyfish/.libs/parse_qual_dna.o jellyfish/.libs/sequence_parser.o jellyfish/.libs/seq_qual_parser.o jellyfish/.libs/backtrace.o jellyfish/.libs/floats.o jellyfish/.libs/dbg.o jellyfish/.libs/allocators_mmap.o jellyfish/.libs/dna_codes.o -L/usr/lib/gcc/aarch64-linux-gnu/10 -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/10/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/10/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/10/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/10/../../../aarch64-linux-gnu/crtn.o -g -O3 -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libjellyfish-1.1.so.1 -o .libs/libjellyfish-1.1.so.1.0.1
libtool: link: (cd ".libs" && rm -f "libjellyfish-1.1.so.1" && ln -s "libjellyfish-1.1.so.1.0.1" "libjellyfish-1.1.so.1")
libtool: link: (cd ".libs" && rm -f "libjellyfish-1.1.so" && ln -s "libjellyfish-1.1.so.1.0.1" "libjellyfish-1.1.so")
libtool: link: ar cr .libs/libjellyfish-1.1.a jellyfish/square_binary_matrix.o jellyfish/err.o jellyfish/misc.o jellyfish/storage.o jellyfish/thread_exec.o jellyfish/time.o jellyfish/file_parser.o jellyfish/read_parser.o jellyfish/parse_read.o jellyfish/half.o jellyfish/mapped_file.o jellyfish/parse_dna.o jellyfish/parse_quake.o jellyfish/parse_qual_dna.o jellyfish/sequence_parser.o jellyfish/seq_qual_parser.o jellyfish/backtrace.o jellyfish/floats.o jellyfish/dbg.o jellyfish/allocators_mmap.o jellyfish/dna_codes.o
libtool: link: ranlib .libs/libjellyfish-1.1.a
libtool: link: ( cd ".libs" && rm -f "libjellyfish-1.1.la" && ln -s "../libjellyfish-1.1.la" "libjellyfish-1.1.la" )
/bin/bash ./libtool --tag=CXX --mode=link g++ -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,--as-needed -latomic -Wl,-z,relro -Wl,-z,now -o bin/jellyfish jellyfish/jellyfish.o jellyfish/stats_main.o jellyfish/hash_merge.o jellyfish/mer_counter.o jellyfish/histo_main.o jellyfish/dump_main.o jellyfish/query_main.o jellyfish/dump_fastq_main.o jellyfish/histo_fastq_main.o jellyfish/cite.o jellyfish/hash_fastq_merge.o jellyfish/yaggo.o libjellyfish-1.1.la
libtool: link: g++ -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,--as-needed -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/jellyfish jellyfish/jellyfish.o jellyfish/stats_main.o jellyfish/hash_merge.o jellyfish/mer_counter.o jellyfish/histo_main.o jellyfish/dump_main.o jellyfish/query_main.o jellyfish/dump_fastq_main.o jellyfish/histo_fastq_main.o jellyfish/cite.o jellyfish/hash_fastq_merge.o jellyfish/yaggo.o -lpthread -latomic ./.libs/libjellyfish-1.1.so
make[3]: Leaving directory '/build/jellyfish1-1.1.11'
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/generate_sequence.o jellyfish/generate_sequence.cc
In file included from jellyfish/generate_sequence.cc:22:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from jellyfish/generate_sequence.cc:23:
./jellyfish/misc.hpp: In function 'int main(int, char**)':
./jellyfish/misc.hpp:106:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | Tptr<T> ptr;
| ^~~
In file included from jellyfish/generate_sequence.cc:24:
./jellyfish/square_binary_matrix.hpp:87:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
87 | free(columns);
| ~~~~^~~~~~~~~
In file included from jellyfish/generate_sequence.cc:23:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
106 | Tptr<T> ptr;
| ^~~
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mersenne.o jellyfish/mersenne.cpp
/bin/bash ./libtool --tag=CXX --mode=link g++ -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,-z,relro -Wl,-z,now -o bin/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o libjellyfish-1.1.la
libtool: link: g++ -g -O3 -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/generate_sequence jellyfish/generate_sequence.o jellyfish/mersenne.o -lpthread ./.libs/libjellyfish-1.1.so
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_offsets_key_value.o `test -f 'unit_tests/test_offsets_key_value.cc' || echo './'`unit_tests/test_offsets_key_value.cc
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_simple_circular_buffer.o `test -f 'unit_tests/test_simple_circular_buffer.cc' || echo './'`unit_tests/test_simple_circular_buffer.cc
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/bin_test_all-test_square_binary_matrix.o `test -f 'unit_tests/test_square_binary_matrix.cc' || echo './'`unit_tests/test_square_binary_matrix.cc
unit_tests/test_square_binary_matrix.cc: In member function 'virtual void SquareBinaryMatrix_Initialization_Test::TestBody()':
unit_tests/test_square_binary_matrix.cc:81:48: warning: catching polymorphic type 'class SquareBinaryMatrix::SingularMatrix' by value [-Wcatch-value=]
81 | } catch(SquareBinaryMatrix::SingularMatrix e) {
| ^
In file included from ./jellyfish/square_binary_matrix.hpp:27,
from unit_tests/test_square_binary_matrix.cc:3:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::ErrorAllocation]':
./jellyfish/square_binary_matrix.hpp:45:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
123 | ~raise_t() { throw err_t(oss.str()); }
| ^~~~~~~~~~~~~~~~~~~~~~
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = SquareBinaryMatrix::MismatchingSize]':
./jellyfish/square_binary_matrix.hpp:54:7: required from here
./jellyfish/err.hpp:123:18: warning: 'throw' will always call 'terminate' [-Wterminate]
./jellyfish/err.hpp:123:18: note: in C++11 destructors default to 'noexcept'
In file included from unit_tests/test_square_binary_matrix.cc:3:
./jellyfish/square_binary_matrix.hpp: In function 'uint64_t* SquareBinaryMatrix::first_alloc(size_t)':
./jellyfish/square_binary_matrix.hpp:46:12: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
46 | return res;
| ^~~
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest -I./unit_tests/gtest/include -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_main_a-gtest_main.o `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest -I./unit_tests/gtest/include -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unit_tests/gtest/src/libgtest_a-gtest-all.o `test -f 'unit_tests/gtest/src/gtest-all.cc' || echo './'`unit_tests/gtest/src/gtest-all.cc
In file included from /usr/include/string.h:495,
from ./unit_tests/gtest/include/gtest/internal/gtest-port.h:195,
from ./unit_tests/gtest/include/gtest/internal/gtest-internal.h:40,
from ./unit_tests/gtest/include/gtest/gtest.h:57,
from unit_tests/gtest/src/gtest-all.cc:39:
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'const char* testing::internal::posix::StrNCpy(char*, const char*, size_t)' at ./unit_tests/gtest/include/gtest/internal/gtest-port.h:1615:17,
inlined from 'char* testing::internal::CloneString(const char*, size_t)' at ./unit_tests/gtest/src/gtest.cc:840:19,
inlined from 'static const char* testing::internal::String::CloneCString(const char*)' at ./unit_tests/gtest/src/gtest.cc:851:39:
/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, long unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from unit_tests/gtest/src/gtest-all.cc:42:
./unit_tests/gtest/src/gtest.cc: In static member function 'static const char* testing::internal::String::CloneCString(const char*)':
./unit_tests/gtest/src/gtest.cc:851:39: note: length computed here
851 | NULL : CloneString(c_str, strlen(c_str));
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
rm -f libgtest.a
ar cru libgtest.a unit_tests/gtest/src/libgtest_a-gtest-all.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgtest.a
rm -f libgtest_main.a
ar cru libgtest_main.a unit_tests/gtest/src/libgtest_main_a-gtest_main.o libgtest.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgtest_main.a
/bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -lpthread -Wl,-z,relro -Wl,-z,now -o bin/test_all unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_square_binary_matrix.o libgtest_main.a libgtest.a libjellyfish-1.1.la
libtool: link: g++ -I./unit_tests/gtest/include -I./unit_tests/gtest -g -O2 -fdebug-prefix-map=/build/jellyfish1-1.1.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/test_all unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_square_binary_matrix.o -lpthread libgtest_main.a libgtest.a ./.libs/libjellyfish-1.1.so
make[2]: Leaving directory '/build/jellyfish1-1.1.11'
make[1]: Leaving directory '/build/jellyfish1-1.1.11'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/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/jellyfish1-1.1.11'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/jellyfish1-1.1.11'
dh_auto_install --destdir=debian/tmp
make -j1 install DESTDIR=/build/jellyfish1-1.1.11/debian/tmp AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/build/jellyfish1-1.1.11'
make[3]: Entering directory '/build/jellyfish1-1.1.11'
/bin/mkdir -p '/build/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-linux-gnu'
/bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-1.1.la '/build/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-linux-gnu'
libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.so.1.0.1 /build/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-1.1.so.1.0.1
libtool: install: (cd /build/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so.1 || { rm -f libjellyfish-1.1.so.1 && ln -s libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so.1; }; })
libtool: install: (cd /build/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-linux-gnu && { ln -s -f libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so || { rm -f libjellyfish-1.1.so && ln -s libjellyfish-1.1.so.1.0.1 libjellyfish-1.1.so; }; })
libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.lai /build/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-1.1.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.a /build/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-1.1.a
libtool: install: chmod 644 /build/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-1.1.a
libtool: install: ranlib /build/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-linux-gnu/libjellyfish-1.1.a
libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-linux-gnu'
/bin/mkdir -p '/build/jellyfish1-1.1.11/debian/tmp/usr/bin'
/bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/build/jellyfish1-1.1.11/debian/tmp/usr/bin'
libtool: warning: 'libjellyfish-1.1.la' has not been installed in '/usr/lib/aarch64-linux-gnu'
libtool: install: /usr/bin/install -c bin/.libs/jellyfish /build/jellyfish1-1.1.11/debian/tmp/usr/bin/jellyfish
/bin/mkdir -p '/build/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/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/jellyfish1-1.1.11/debian/tmp/usr/include/jellyfish-1.1.11/jellyfish'
/bin/mkdir -p '/build/jellyfish1-1.1.11/debian/tmp/usr/share/man/man1'
/usr/bin/install -c -m 644 'doc/jellyfish.man' '/build/jellyfish1-1.1.11/debian/tmp/usr/share/man/man1/jellyfish.1'
/bin/mkdir -p '/build/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig'
/usr/bin/install -c -m 644 jellyfish-1.1.pc '/build/jellyfish1-1.1.11/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig'
make[3]: Leaving directory '/build/jellyfish1-1.1.11'
make[2]: Leaving directory '/build/jellyfish1-1.1.11'
make[1]: Leaving directory '/build/jellyfish1-1.1.11'
debian/rules override_dh_install
make[1]: Entering directory '/build/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/jellyfish1-1.1.11'
dh_installdocs
dh_installchangelogs
debian/rules override_dh_installman
make[1]: Entering directory '/build/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/jellyfish1-1.1.11'
dh_lintian
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: symbol pthread_join used by debian/jellyfish1/usr/lib/aarch64-linux-gnu/libjellyfish-1.1.so.1.0.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol pthread_create used by debian/jellyfish1/usr/lib/aarch64-linux-gnu/libjellyfish-1.1.so.1.0.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol pthread_cancel used by debian/jellyfish1/usr/lib/aarch64-linux-gnu/libjellyfish-1.1.so.1.0.1 found in none of the libraries
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'jellyfish1' in '../jellyfish1_1.1.11-5_arm64.deb'.
dpkg-deb: building package 'jellyfish1-dbgsym' in '../jellyfish1-dbgsym_1.1.11-5_arm64.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../jellyfish1_1.1.11-5_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/30987 and its subdirectories
I: Current time: Tue Jul 13 00:29:58 -12 2021
I: pbuilder-time-stamp: 1626179398
Tue Jul 13 12:29:59 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink9-arm64.debian.net.
Tue Jul 13 12:29:59 UTC 2021 I: Preparing to do remote build '2' on codethink9-arm64.debian.net.
Tue Jul 13 12:33:53 UTC 2021 I: Deleting $TMPDIR on codethink9-arm64.debian.net.
Tue Jul 13 12:33:53 UTC 2021 I: jellyfish1_1.1.11-5_arm64.changes:
Format: 1.8
Date: Thu, 26 Nov 2020 07:52:51 +0100
Source: jellyfish1
Binary: jellyfish1 jellyfish1-dbgsym
Architecture: arm64
Version: 1.1.11-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
jellyfish1 - count k-mers in DNA sequences
Changes:
jellyfish1 (1.1.11-5) unstable; urgency=medium
.
* Standards-Version: 4.5.1 (routine-update)
* debhelper-compat 13 (routine-update)
* Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine-
update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Use secure URI in Homepage field.
Checksums-Sha1:
3a37a896db395be8cc2f9402baecc3fb9483df02 1135080 jellyfish1-dbgsym_1.1.11-5_arm64.deb
c9719cdafc1c7d389f489cd5ce44577d8e2a04b9 4865 jellyfish1_1.1.11-5_arm64.buildinfo
88ceb329f2f4779d62fe944be34f0e55b5ff6795 131524 jellyfish1_1.1.11-5_arm64.deb
Checksums-Sha256:
d783522f4583dece67cc8949ea102f0b9fcf59c7d8aa94873f6a4991dd6b3da6 1135080 jellyfish1-dbgsym_1.1.11-5_arm64.deb
a0ff0b69a60208fb8794b2e908563ba3095afbeab367d8892192eba27d91c5bb 4865 jellyfish1_1.1.11-5_arm64.buildinfo
f36e1ac44a719193e1b558b3d743b12a66fdd47d5a3a0602d8c6b81407a66491 131524 jellyfish1_1.1.11-5_arm64.deb
Files:
809522e1dd704051b74075f52c647877 1135080 debug optional jellyfish1-dbgsym_1.1.11-5_arm64.deb
ca39fe993f76c1404f7cc8357ed2f671 4865 science optional jellyfish1_1.1.11-5_arm64.buildinfo
5f2e22b86045f6b6f225f221ef937589 131524 science optional jellyfish1_1.1.11-5_arm64.deb
Tue Jul 13 12:33:54 UTC 2021 I: diffoscope 177 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.E2nu0kmgZb/jellyfish1_1.1.11-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.E2nu0kmgZb/jellyfish1_1.1.11-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.E2nu0kmgZb/jellyfish1_1.1.11-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.E2nu0kmgZb/b1/jellyfish1_1.1.11-5_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.E2nu0kmgZb/b2/jellyfish1_1.1.11-5_arm64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.266s)
0.266s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.029s)
0.029s 10 calls diffoscope.comparators.binary.FilesystemFile
0.000s 8 calls abc.DotChangesFile
Tue Jul 13 12:33:56 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists.
Tue Jul 13 12:33:56 UTC 2021 I: jellyfish1 from bullseye built successfully and reproducibly on arm64.
Tue Jul 13 12:33:57 UTC 2021 I: Submitting .buildinfo files to external archives:
Tue Jul 13 12:33:57 UTC 2021 I: Submitting 8.0K b1/jellyfish1_1.1.11-5_arm64.buildinfo.asc
Tue Jul 13 12:33:58 UTC 2021 I: Submitting 8.0K b2/jellyfish1_1.1.11-5_arm64.buildinfo.asc
Tue Jul 13 12:33:59 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Tue Jul 13 12:33:59 UTC 2021 I: Done submitting .buildinfo files.
Tue Jul 13 12:33:59 UTC 2021 I: Removing signed jellyfish1_1.1.11-5_arm64.buildinfo.asc files:
removed './b1/jellyfish1_1.1.11-5_arm64.buildinfo.asc'
removed './b2/jellyfish1_1.1.11-5_arm64.buildinfo.asc'