jellyfish1 →
1.1.11-5 →
armhf → 2020-12-01 10:21:55
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| jellyfish1 1.1.11-5 (armhf) Tue, 01 Dec 2020 10:11:22 +0000 |
+==============================================================================+
Package: jellyfish1
Version: 1.1.11-5
Source Version: 1.1.11-5
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-dc9530bd-bc86-434f-954b-088dd34c694f' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/jellyfish1-49oenB/resolver-tEQyp2' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.9 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.8 MB in 18s (1361 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'jellyfish1' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/jellyfish1.git
Please use:
git clone https://salsa.debian.org/med-team/jellyfish1.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1074 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main jellyfish1 1.1.11-5 (dsc) [2015 B]
Get:2 http://172.17.0.1/private bullseye-staging/main jellyfish1 1.1.11-5 (tar) [1067 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main jellyfish1 1.1.11-5 (diff) [5016 B]
Fetched 1074 kB in 2s (710 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/jellyfish1-49oenB/jellyfish1-1.1.11' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/jellyfish1-49oenB' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [370 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [452 B]
Fetched 1779 B in 0s (48.5 kB/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl
libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu67 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db po-debconf sensible-utils
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl
libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu67 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils
0 upgraded, 34 newly installed, 0 to remove and 33 not upgraded.
Need to get 18.6 MB of archives.
After this operation, 68.4 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [872 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf bsdextrautils armhf 2.36.1-1 [133 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-1 [162 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.3-1 [1176 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.2 [578 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 18.6 MB in 5s (4057 kB/s)
Selecting previously unselected package bsdextrautils.
(Reading database ... 12445 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.36.1-1_armhf.deb ...
Unpacking bsdextrautils (2.36.1-1) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../02-groff-base_1.22.4-5_armhf.deb ...
Unpacking groff-base (1.22.4-5) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../03-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.9.3-2_armhf.deb ...
Unpacking man-db (2.9.3-2) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../05-sensible-utils_0.0.12+nmu1_all.deb ...
Unpacking sensible-utils (0.0.12+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../06-libmagic-mgc_1%3a5.38-5_armhf.deb ...
Unpacking libmagic-mgc (1:5.38-5) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../07-libmagic1_1%3a5.38-5_armhf.deb ...
Unpacking libmagic1:armhf (1:5.38-5) ...
Selecting previously unselected package file.
Preparing to unpack .../08-file_1%3a5.38-5_armhf.deb ...
Unpacking file (1:5.38-5) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../09-gettext-base_0.19.8.1-10_armhf.deb ...
Unpacking gettext-base (0.19.8.1-10) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../10-libsigsegv2_2.12-2_armhf.deb ...
Unpacking libsigsegv2:armhf (2.12-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../11-m4_1.4.18-4_armhf.deb ...
Unpacking m4 (1.4.18-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../12-autoconf_2.69-11.1_all.deb ...
Unpacking autoconf (2.69-11.1) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../13-autotools-dev_20180224.1_all.deb ...
Unpacking autotools-dev (20180224.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../14-automake_1%3a1.16.2-4_all.deb ...
Unpacking automake (1:1.16.2-4) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../15-autopoint_0.19.8.1-10_all.deb ...
Unpacking autopoint (0.19.8.1-10) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.4.6-14_all.deb ...
Unpacking libtool (2.4.6-14) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../17-dh-autoreconf_19_all.deb ...
Unpacking dh-autoreconf (19) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../18-libdebhelper-perl_13.2.1_all.deb ...
Unpacking libdebhelper-perl (13.2.1) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../20-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.9.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.9.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../22-dh-strip-nondeterminism_1.9.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.9.0-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../23-libelf1_0.182-1_armhf.deb ...
Unpacking libelf1:armhf (0.182-1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../24-dwz_0.13-5_armhf.deb ...
Unpacking dwz (0.13-5) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../25-libglib2.0-0_2.66.3-1_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.66.3-1) ...
Selecting previously unselected package libicu67:armhf.
Preparing to unpack .../26-libicu67_67.1-4_armhf.deb ...
Unpacking libicu67:armhf (67.1-4) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../27-libxml2_2.9.10+dfsg-6.2_armhf.deb ...
Unpacking libxml2:armhf (2.9.10+dfsg-6.2) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../28-libcroco3_0.6.13-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.13-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../29-gettext_0.19.8.1-10_armhf.deb ...
Unpacking gettext (0.19.8.1-10) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../30-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../31-po-debconf_1.0.21_all.deb ...
Unpacking po-debconf (1.0.21) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../32-debhelper_13.2.1_all.deb ...
Unpacking debhelper (13.2.1) ...
Selecting previously unselected package sbuild-build-depends-main-dummy.
Preparing to unpack .../33-sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up bsdextrautils (2.36.1-1) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-4) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.66.3-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.2.1) ...
Setting up libmagic1:armhf (1:5.38-5) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-5) ...
Setting up autotools-dev (20180224.1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libelf1:armhf (0.182-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.2) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libtool (2.4.6-14) ...
Setting up m4 (1.4.18-4) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up automake (1:1.16.2-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up debhelper (13.2.1) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-4+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.35.1-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-16+rpi1 gcc-10_10.2.0-16+rpi1 libc6-dev_2.31-4+rpi1 libstdc++-10-dev_10.2.0-16+rpi1 libstdc++6_10.2.0-16+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.11 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1~rc2-1 binutils_2.35.1-2+rpi1 binutils-arm-linux-gnueabihf_2.35.1-2+rpi1 binutils-common_2.35.1-2+rpi1 bsdextrautils_2.36.1-1 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.0-16+rpi1 dash_0.5.11+git20200708+dd9ef66-2 debconf_1.5.74 debhelper_13.2.1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1 file_1:5.38-5 findutils_4.7.0+git20201010-2 g++_4:10.2.0-1+rpi1 g++-10_10.2.0-16+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.0-16+rpi1 gcc-10-base_10.2.0-16+rpi1 gcc-7-base_7.5.0-6+rpi1+b1 gcc-8-base_8.4.0-4+rpi1+b1 gcc-9-base_9.3.0-18+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg6.0_2.1.11 libarchive-zip-perl_1.68-1 libasan6_10.2.0-16+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-16+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1 libbinutils_2.35.1-2+rpi1 libblkid1_2.36-3 libbz2-1.0_1.0.8-4 libc-bin_2.31-4+rpi1 libc-dev-bin_2.31-4+rpi1 libc6_2.31-4+rpi1 libc6-dev_2.31-4+rpi1 libcap-ng0_0.7.9-2.2 libcc1-0_10.2.0-16+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-2+rpi1 libctf0_2.35.1-2+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.255 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5+rpi1 libelf1_0.182-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-16+rpi1 libgcc-s1_10.2.0-16+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.3-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-16+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-3 libisl22_0.22.1-1 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 libldap-2.4-2_2.4.56+dfsg-1+rpi1+b1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.21-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.32_5.32.0-5 libpipeline1_1.5.3-1 libreadline8_8.1~rc2-2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.0-3+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssl1.1_1.1.1h-1 libstdc++-10-dev_10.2.0-16+rpi1 libstdc++6_10.2.0-16+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.6-2+rpi1 libtasn1-6_4.16.0-2 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20200918-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-16+rpi1 libuchardet0_0.0.7-1 libudev1_246.6-2+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libxml2_2.9.10+dfsg-6.2 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-3 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.32.0-5 perl-base_5.32.0-5 perl-modules-5.32_5.32.0-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.1~rc2-2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.30+dfsg-7 tzdata_2020d-1 util-linux_2.36-3 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----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
Checksums-Sha256:
496645d96b08ba35db1f856d857a159798c73cbc1eccb852ef1b253d1678c8e2 1067138 jellyfish1_1.1.11.orig.tar.gz
37eae87742011610c68078ac1fda923bedcba924fca4161969493f8ca84819da 5016 jellyfish1_1.1.11-5.debian.tar.xz
Files:
dc994ea8b0896156500ea8c648f24846 1067138 jellyfish1_1.1.11.orig.tar.gz
d49be598ea2ed67eedb246e5db1878cb 5016 jellyfish1_1.1.11-5.debian.tar.xz
-----BEGIN PGP SIGNATURE-----
iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+/VbkRHHRpbGxlQGRl
Ymlhbi5vcmcACgkQV4oElNHGRtGMPg//RYlbAb0zUJI+Ww/w5Od9wEWqyMUDt7IA
mwKdB1NHB3zFtkBD6Ayg5pezNzFXfR8dNvwUy347Ch/k2md9DgRtugxgRbcT4139
K6X+vZ0bNXyKIE/E+O2pp6rmneYH3cpirRK7K6JyJW2wyy4et9m5Iow5z+SXHUU7
uXNbpJmlOHyhKSHibUV1Nm/SuMXQ6CL0MqDRAC9NeaA5UOsVpualV+tHudWzIzMm
tcOe+tQnKcjBXPLXhHel3UywDOtTpLQ7BtKK7+mP6KNrVZq1yPDByNXHVgdEUx5q
Ocs19QKzyclyL45mXgy3xxZij7jyeAdPRfuUwaSt/XvMzxgPPMlyqYYzCMv+jkeV
mHZjfUyXTLBmamw2PdLzn73G70JUuyyvWGH02tdd63DcmVpQT8J/UXjQziNoGsuA
QmL7ZHsutO791XGATknPmR/DbvoXdX4oA5YS3z0ciwqyXbfrBxTTvxcOLgOIYzDV
QfY2vW63Nxe/mVJnkHZZqv+QyXEjR4bHkaAsoDdzZlVyTHIhQjlPlPYDunuY2KOs
1SZGaKWtZ/FjIzGwLuo1HFG/1dL7LiyX+ZxpmPs4ADVNhqtmo6AiwnqSeo6Z/dN1
ADFmsdgKGhrQYEjAXLtAMS0pKidfmkF8t9CGy2PkQfpCBs1zVr53563xwUFqR71b
lr7EuThz42k=
=rg+M
-----END PGP SIGNATURE-----
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.YZU1_EBb/trustedkeys.kbx': General error
gpgv: Signature made Thu Nov 26 07:14:01 2020 UTC
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 /<<PKGBUILDDIR>>
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
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=1ec3ff19654148fab3a02153247d5928
JOURNAL_STREAM=8:145870
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-dc9530bd-bc86-434f-954b-088dd34c694f
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c31126
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package jellyfish1
dpkg-buildpackage: info: source version 1.1.11-5
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
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 '/<<PKGBUILDDIR>>'
dh_auto_configure
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
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 arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf 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... no
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 '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
make all-am
make[3]: Entering directory '/<<PKGBUILDDIR>>'
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/stats_main.o jellyfish/stats_main.cc
In file included from ./jellyfish/mer_counting.hpp:31,
from jellyfish/stats_main.cc:26:
./jellyfish/compacted_hash.hpp: In member function ‘void jellyfish::compacted_hash::writer<storage_t>::write_header(std::ostream*) const’:
./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/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 = 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 long unsigned int, atomic::gcc, allocators::mmap>; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array<long 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 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/stats_main.cc:25:
./jellyfish/misc.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array<long long unsigned int, atomic::gcc, allocators::mmap>]’:
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | Tptr<T> ptr;
| ^~~
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/hash_merge.o jellyfish/hash_merge.cc
In file included from ./jellyfish/mer_counting.hpp:31,
from jellyfish/hash_merge.cc:34:
./jellyfish/compacted_hash.hpp: In member function ‘void jellyfish::compacted_hash::writer<storage_t>::write_header(std::ostream*) const’:
./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 = 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 long unsigned int, long 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 = 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_merge.cc:33:
./jellyfish/misc.hpp: In copy constructor ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’:
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/mer_counter.o jellyfish/mer_counter.cc
In file included from ./jellyfish/mer_counting.hpp:31,
from jellyfish/mer_counter.cc:38:
./jellyfish/compacted_hash.hpp: In member function ‘void jellyfish::compacted_hash::writer<storage_t>::write_header(std::ostream*) const’:
./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 = 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 long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap; size_t = unsigned int; uint_t = long 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 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 = 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 long unsigned int; size_t = 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 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 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 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 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 long unsigned int, jellyfish::Float, jellyfish::aligned_values::array<long 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 long unsigned int; val_t = jellyfish::Float; ary_t = jellyfish::aligned_values::array<long 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 long unsigned int, jellyfish::Float, jellyfish::aligned_values::array<long 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 long unsigned int, jellyfish::capped_integer<unsigned int>, jellyfish::direct_indexing::array<long 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 long unsigned int; val_t = jellyfish::capped_integer<unsigned int>; ary_t = jellyfish::direct_indexing::array<long 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 long unsigned int, jellyfish::capped_integer<unsigned int>, jellyfish::direct_indexing::array<long 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 long unsigned int, long long unsigned int, jellyfish::invertible_hash::array<long 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 long unsigned int; val_t = long long unsigned int; ary_t = jellyfish::invertible_hash::array<long 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 long unsigned int, long long unsigned int, jellyfish::invertible_hash::array<long 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 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;
| ^~~
./jellyfish/misc.hpp: In member function ‘void jellyfish::invertible_hash::array<word, atomic_t, mem_block_t>::set_matrix(SquareBinaryMatrix&) [with word = long long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]’:
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/histo_main.o jellyfish/histo_main.cc
In file included from ./jellyfish/mer_counting.hpp:31,
from jellyfish/histo_main.cc:27:
./jellyfish/compacted_hash.hpp: In member function ‘void jellyfish::compacted_hash::writer<storage_t>::write_header(std::ostream*) const’:
./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/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 = 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 long unsigned int, atomic::gcc, allocators::mmap>; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array<long 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 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/histo_main.cc:26:
./jellyfish/misc.hpp: In copy constructor ‘SquareBinaryMatrix::SquareBinaryMatrix(const SquareBinaryMatrix&)’:
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | Tptr<T> ptr;
| ^~~
./jellyfish/misc.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array<long long unsigned int, atomic::gcc, allocators::mmap>]’:
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dump_main.o jellyfish/dump_main.cc
In file included from ./jellyfish/mer_counting.hpp:31,
from jellyfish/dump_main.cc:26:
./jellyfish/compacted_hash.hpp: In member function ‘void jellyfish::compacted_hash::writer<storage_t>::write_header(std::ostream*) const’:
./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/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 = 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 long unsigned int, atomic::gcc, allocators::mmap>; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array<long 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 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/dump_main.cc:25:
./jellyfish/misc.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array<long long unsigned int, atomic::gcc, allocators::mmap>]’:
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | Tptr<T> ptr;
| ^~~
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/query_main.o jellyfish/query_main.cc
In file included from ./jellyfish/mer_counting.hpp:31,
from jellyfish/query_main.cc:24:
./jellyfish/compacted_hash.hpp: In member function ‘void jellyfish::compacted_hash::writer<storage_t>::write_header(std::ostream*) const’:
./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/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 = 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 long unsigned int, atomic::gcc, allocators::mmap>; jellyfish::raw_hash::query<_storage_t>::storage_t = jellyfish::invertible_hash::array<long 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 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/query_main.cc:23:
./jellyfish/misc.hpp: In static member function ‘static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array<long long unsigned int, atomic::gcc, allocators::mmap>]’:
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | Tptr<T> ptr;
| ^~~
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/dump_fastq_main.o jellyfish/dump_fastq_main.cc
In file included from ./jellyfish/mer_counting.hpp:31,
from jellyfish/dump_fastq_main.cc:27:
./jellyfish/compacted_hash.hpp: In member function ‘void jellyfish::compacted_hash::writer<storage_t>::write_header(std::ostream*) const’:
./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/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 = 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/dump_fastq_main.cc:26:
./jellyfish/misc.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]’:
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | Tptr<T> ptr;
| ^~~
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/histo_fastq_main.o jellyfish/histo_fastq_main.cc
In file included from ./jellyfish/mer_counting.hpp:31,
from jellyfish/histo_fastq_main.cc:28:
./jellyfish/compacted_hash.hpp: In member function ‘void jellyfish::compacted_hash::writer<storage_t>::write_header(std::ostream*) const’:
./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/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 = 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/histo_fastq_main.cc:27:
./jellyfish/misc.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]’:
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | Tptr<T> ptr;
| ^~~
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o jellyfish/hash_fastq_merge.o jellyfish/hash_fastq_merge.cc
In file included from ./jellyfish/mer_counting.hpp:31,
from jellyfish/hash_fastq_merge.cc:19:
./jellyfish/compacted_hash.hpp: In member function ‘void jellyfish::compacted_hash::writer<storage_t>::write_header(std::ostream*) const’:
./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_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 long unsigned int, jellyfish::Float, jellyfish::aligned_values::array<long 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 long unsigned int; val_t = jellyfish::Float; ary_t = jellyfish::aligned_values::array<long 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 = 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 long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap; size_t = unsigned int; uint_t = long 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 long unsigned int; _val_t = jellyfish::Float; atomic = atomic::gcc; mem_block_t = allocators::mmap; size_t = unsigned int; uint_t = long 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_fastq_merge.cc:18:
./jellyfish/misc.hpp: In static member function ‘static storage_t* jellyfish::fastq_hash::raw_dumper<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]’:
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
106 | Tptr<T> ptr;
| ^~~
./jellyfish/misc.hpp:106:11: warning: ‘ptr’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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:20:
./jellyfish/misc.hpp: In member function ‘SquareBinaryMatrix SquareBinaryMatrix::transpose() const’:
./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/square_binary_matrix.cc:21:
./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;
| ^~~
In file included from jellyfish/square_binary_matrix.cc:21:
./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/square_binary_matrix.cc:20:
./jellyfish/misc.hpp:106:11: note: ‘ptr’ was declared here
106 | Tptr<T> ptr;
| ^~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 = 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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 = 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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 = 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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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/arm-linux-gnueabihf 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/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/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/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/10/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>'
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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:24:
./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;
| ^~~
In file included from /usr/include/c++/10/vector:72,
from jellyfish/generate_sequence.cc:18:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long unsigned int>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function ‘void generate_sequence_args::parse(int, char**)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, 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=/<<PKGBUILDDIR>>=. -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=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# dh_auto_test && true
echo "****************************************************** do not test for the moment ******************************************************"
****************************************************** do not test for the moment ******************************************************
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install --destdir=debian/tmp
make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
/bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-1.1.la '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.so.1.0.1 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-1.1.so.1.0.1
libtool: install: (cd /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf && { 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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf && { 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 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-1.1.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-1.1.a /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-1.1.a
libtool: install: chmod 644 /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-1.1.a
libtool: install: ranlib /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libjellyfish-1.1.a
libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
libtool: warning: 'libjellyfish-1.1.la' has not been installed in '/usr/lib/arm-linux-gnueabihf'
libtool: install: /usr/bin/install -c bin/.libs/jellyfish /<<PKGBUILDDIR>>/debian/tmp/usr/bin/jellyfish
/bin/mkdir -p '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/debian/tmp/usr/include/jellyfish-1.1.11/jellyfish'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1'
/usr/bin/install -c -m 644 'doc/jellyfish.man' '/<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1/jellyfish.1'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
/usr/bin/install -c -m 644 jellyfish-1.1.pc '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installman
mv debian/jellyfish1/usr/share/man/man1/jellyfish.1 debian/jellyfish1/usr/share/man/man1/jellyfish1.1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_lintian -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -a
dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/jellyfish1/usr/lib/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/libjellyfish-1.1.so.1.0.1 found in none of the libraries
dpkg-shlibdeps: warning: symbol pthread_join used by debian/jellyfish1/usr/lib/arm-linux-gnueabihf/libjellyfish-1.1.so.1.0.1 found in none of the libraries
dpkg-shlibdeps: warning: debian/jellyfish1/usr/lib/jellyfish1/jellyfish contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'jellyfish1-dbgsym' in '../jellyfish1-dbgsym_1.1.11-5_armhf.deb'.
dpkg-deb: building package 'jellyfish1' in '../jellyfish1_1.1.11-5_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> >../jellyfish1_1.1.11-5_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-12-01T10:21:41Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
jellyfish1_1.1.11-5_armhf.changes:
----------------------------------
Format: 1.8
Date: Thu, 26 Nov 2020 07:52:51 +0100
Source: jellyfish1
Binary: jellyfish1 jellyfish1-dbgsym
Architecture: armhf
Version: 1.1.11-5
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.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:
12cb62991584d3be64326b5458867facf206b0cf 1104920 jellyfish1-dbgsym_1.1.11-5_armhf.deb
aefbd50ce2047f480ec5b0c2e60394c8181ca89b 5029 jellyfish1_1.1.11-5_armhf.buildinfo
b692053379e47f55a2168e19dc23571032cee839 122384 jellyfish1_1.1.11-5_armhf.deb
Checksums-Sha256:
21ad5e757b51b650a4ae5b74ca1a9063d6ca9814335c5630b79fc2aa3cd5159f 1104920 jellyfish1-dbgsym_1.1.11-5_armhf.deb
92a439ef7c77f1d7652d481aaddaba925fb60af0dc75c6e684c1ccf839b4f0a6 5029 jellyfish1_1.1.11-5_armhf.buildinfo
379b57ac25c525904e0c7020f8109f0a6b2482c4c2241451f766af0ed9f61643 122384 jellyfish1_1.1.11-5_armhf.deb
Files:
5d2b5da341b7ff6d58057211d8eb9f5d 1104920 debug optional jellyfish1-dbgsym_1.1.11-5_armhf.deb
f7a4f1be983d2eb969202b367831290c 5029 science optional jellyfish1_1.1.11-5_armhf.buildinfo
58e8f1e16c33a857f2bf559add624d9c 122384 science optional jellyfish1_1.1.11-5_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: jellyfish1
Binary: jellyfish1 jellyfish1-dbgsym
Architecture: armhf
Version: 1.1.11-5
Checksums-Md5:
5d2b5da341b7ff6d58057211d8eb9f5d 1104920 jellyfish1-dbgsym_1.1.11-5_armhf.deb
58e8f1e16c33a857f2bf559add624d9c 122384 jellyfish1_1.1.11-5_armhf.deb
Checksums-Sha1:
12cb62991584d3be64326b5458867facf206b0cf 1104920 jellyfish1-dbgsym_1.1.11-5_armhf.deb
b692053379e47f55a2168e19dc23571032cee839 122384 jellyfish1_1.1.11-5_armhf.deb
Checksums-Sha256:
21ad5e757b51b650a4ae5b74ca1a9063d6ca9814335c5630b79fc2aa3cd5159f 1104920 jellyfish1-dbgsym_1.1.11-5_armhf.deb
379b57ac25c525904e0c7020f8109f0a6b2482c4c2241451f766af0ed9f61643 122384 jellyfish1_1.1.11-5_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Tue, 01 Dec 2020 10:21:40 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.69-11.1),
automake (= 1:1.16.2-4),
autopoint (= 0.19.8.1-10),
autotools-dev (= 20180224.1),
base-files (= 11+rpi1),
base-passwd (= 3.5.48),
bash (= 5.1~rc2-1),
binutils (= 2.35.1-2+rpi1),
binutils-arm-linux-gnueabihf (= 2.35.1-2+rpi1),
binutils-common (= 2.35.1-2+rpi1),
bsdextrautils (= 2.36.1-1),
bsdutils (= 1:2.36-3),
build-essential (= 12.8),
bzip2 (= 1.0.8-4),
coreutils (= 8.32-4),
cpp (= 4:10.2.0-1+rpi1),
cpp-10 (= 10.2.0-16+rpi1),
dash (= 0.5.11+git20200708+dd9ef66-2),
debconf (= 1.5.74),
debhelper (= 13.2.1),
debianutils (= 4.11.2),
dh-autoreconf (= 19),
dh-strip-nondeterminism (= 1.9.0-1),
diffutils (= 1:3.7-3),
dpkg (= 1.20.5+rpi1),
dpkg-dev (= 1.20.5+rpi1),
dwz (= 0.13-5),
file (= 1:5.38-5),
findutils (= 4.7.0+git20201010-2),
g++ (= 4:10.2.0-1+rpi1),
g++-10 (= 10.2.0-16+rpi1),
gcc (= 4:10.2.0-1+rpi1),
gcc-10 (= 10.2.0-16+rpi1),
gcc-10-base (= 10.2.0-16+rpi1),
gettext (= 0.19.8.1-10),
gettext-base (= 0.19.8.1-10),
grep (= 3.6-1),
groff-base (= 1.22.4-5),
gzip (= 1.10-2),
hostname (= 3.23),
init-system-helpers (= 1.58),
intltool-debian (= 0.35.0+20060710.5),
libacl1 (= 2.2.53-8),
libarchive-zip-perl (= 1.68-1),
libasan6 (= 10.2.0-16+rpi1),
libatomic1 (= 10.2.0-16+rpi1),
libattr1 (= 1:2.4.48-5),
libaudit-common (= 1:2.8.5-3.1),
libaudit1 (= 1:2.8.5-3.1),
libbinutils (= 2.35.1-2+rpi1),
libblkid1 (= 2.36-3),
libbz2-1.0 (= 1.0.8-4),
libc-bin (= 2.31-4+rpi1),
libc-dev-bin (= 2.31-4+rpi1),
libc6 (= 2.31-4+rpi1),
libc6-dev (= 2.31-4+rpi1),
libcap-ng0 (= 0.7.9-2.2),
libcc1-0 (= 10.2.0-16+rpi1),
libcom-err2 (= 1.45.6-1),
libcroco3 (= 0.6.13-1),
libcrypt-dev (= 1:4.4.17-1),
libcrypt1 (= 1:4.4.17-1),
libctf-nobfd0 (= 2.35.1-2+rpi1),
libctf0 (= 2.35.1-2+rpi1),
libdb5.3 (= 5.3.28+dfsg1-0.6),
libdebconfclient0 (= 0.255),
libdebhelper-perl (= 13.2.1),
libdpkg-perl (= 1.20.5+rpi1),
libelf1 (= 0.182-1),
libffi7 (= 3.3-5),
libfile-stripnondeterminism-perl (= 1.9.0-1),
libgcc-10-dev (= 10.2.0-16+rpi1),
libgcc-s1 (= 10.2.0-16+rpi1),
libgcrypt20 (= 1.8.7-2),
libgdbm-compat4 (= 1.18.1-5.1),
libgdbm6 (= 1.18.1-5.1),
libglib2.0-0 (= 2.66.3-1),
libgmp10 (= 2:6.2.0+dfsg-6),
libgomp1 (= 10.2.0-16+rpi1),
libgpg-error0 (= 1.38-2),
libgssapi-krb5-2 (= 1.17-10+b3),
libicu67 (= 67.1-4),
libisl22 (= 0.22.1-1),
libk5crypto3 (= 1.17-10+b3),
libkeyutils1 (= 1.6.1-2),
libkrb5-3 (= 1.17-10+b3),
libkrb5support0 (= 1.17-10+b3),
liblz4-1 (= 1.9.2-2),
liblzma5 (= 5.2.4-1),
libmagic-mgc (= 1:5.38-5),
libmagic1 (= 1:5.38-5),
libmount1 (= 2.36-3),
libmpc3 (= 1.2.0-1),
libmpfr6 (= 4.1.0-3),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libnss-nis (= 3.1-4),
libnss-nisplus (= 1.3-4),
libpam-modules (= 1.3.1-5),
libpam-modules-bin (= 1.3.1-5),
libpam-runtime (= 1.3.1-5),
libpam0g (= 1.3.1-5),
libpcre2-8-0 (= 10.34-7),
libpcre3 (= 2:8.39-13),
libperl5.32 (= 5.32.0-5),
libpipeline1 (= 1.5.3-1),
libseccomp2 (= 2.5.0-3+rpi1),
libselinux1 (= 3.1-2),
libsigsegv2 (= 2.12-2),
libsmartcols1 (= 2.36-3),
libssl1.1 (= 1.1.1h-1),
libstdc++-10-dev (= 10.2.0-16+rpi1),
libstdc++6 (= 10.2.0-16+rpi1),
libsub-override-perl (= 0.09-2),
libsystemd0 (= 246.6-2+rpi1),
libtinfo6 (= 6.2+20200918-1),
libtirpc-common (= 1.2.6-3),
libtirpc-dev (= 1.2.6-3),
libtirpc3 (= 1.2.6-3),
libtool (= 2.4.6-14),
libubsan1 (= 10.2.0-16+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 246.6-2+rpi1),
libunistring2 (= 0.9.10-4),
libuuid1 (= 2.36-3),
libxml2 (= 2.9.10+dfsg-6.2),
libzstd1 (= 1.4.5+dfsg-4+rpi1),
linux-libc-dev (= 5.7.10-1+rpi1),
login (= 1:4.8.1-1),
lsb-base (= 11.1.0+rpi1),
m4 (= 1.4.18-4),
make (= 4.3-4),
man-db (= 2.9.3-2),
mawk (= 1.3.4.20200120-2),
ncurses-base (= 6.2+20200918-1),
ncurses-bin (= 6.2+20200918-1),
patch (= 2.7.6-6),
perl (= 5.32.0-5),
perl-base (= 5.32.0-5),
perl-modules-5.32 (= 5.32.0-5),
po-debconf (= 1.0.21),
sed (= 4.7-1),
sensible-utils (= 0.0.12+nmu1),
sysvinit-utils (= 2.96-5),
tar (= 1.30+dfsg-7),
util-linux (= 2.36-3),
xz-utils (= 5.2.4-1),
zlib1g (= 1:1.2.11.dfsg-2)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1606373571"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
jellyfish1-dbgsym_1.1.11-5_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 1104920 bytes: control archive=652 bytes.
426 bytes, 12 lines control
302 bytes, 3 lines md5sums
Package: jellyfish1-dbgsym
Source: jellyfish1
Version: 1.1.11-5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1196
Depends: jellyfish1 (= 1.1.11-5)
Section: debug
Priority: optional
Description: debug symbols for jellyfish1
Build-Ids: 3fd0ace3ea8649e44bc9be75b5b828c16afb7a89 e28f4387e0dc387a850cc826c37ed39d8c4eb5c8
drwxr-xr-x root/root 0 2020-11-26 06:52 ./
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/lib/
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/lib/debug/.build-id/3f/
-rw-r--r-- root/root 976788 2020-11-26 06:52 ./usr/lib/debug/.build-id/3f/d0ace3ea8649e44bc9be75b5b828c16afb7a89.debug
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/lib/debug/.build-id/e2/
-rw-r--r-- root/root 204704 2020-11-26 06:52 ./usr/lib/debug/.build-id/e2/8f4387e0dc387a850cc826c37ed39d8c4eb5c8.debug
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 28684 2020-11-26 06:52 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/jellyfish1.debug
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/share/
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-11-26 06:52 ./usr/share/doc/jellyfish1-dbgsym -> jellyfish1
jellyfish1_1.1.11-5_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 122384 bytes: control archive=1352 bytes.
1310 bytes, 28 lines control
507 bytes, 7 lines md5sums
42 bytes, 1 lines shlibs
67 bytes, 2 lines triggers
Package: jellyfish1
Version: 1.1.11-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 583
Depends: libc6 (>= 2.4), libgcc-s1 (>= 3.5), libstdc++6 (>= 5.2)
Enhances: kraken
Section: science
Priority: optional
Homepage: https://www.cbcb.umd.edu/software/jellyfish/
Description: count k-mers in DNA sequences
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences
of all such substrings is a central step in many analyses of DNA
sequence. JELLYFISH can count k-mers using an order of magnitude less
memory and an order of magnitude faster than other k-mer counting
packages by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase
parallelism.
.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA
files containing DNA sequences. It outputs its k-mer counts in an
binary format, which can be translated into a human-readable text
format using the "jellyfish dump" command.
.
This is the latest version of the 1.x series of jellyfish which is
used by some other applications that are not compatible with version
2.x which is provided inside the jellyfish package.
drwxr-xr-x root/root 0 2020-11-26 06:52 ./
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/bin/
lrwxrwxrwx root/root 0 2020-11-26 06:52 ./usr/bin/jellyfish1 -> ../lib/jellyfish1/jellyfish
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/lib/
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2020-11-26 06:52 ./usr/lib/arm-linux-gnueabihf/libjellyfish-1.1.so.1 -> libjellyfish-1.1.so.1.0.1
-rw-r--r-- root/root 350764 2020-11-26 06:52 ./usr/lib/arm-linux-gnueabihf/libjellyfish-1.1.so.1.0.1
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/lib/jellyfish1/
-rwxr-xr-x root/root 212672 2020-11-26 06:52 ./usr/lib/jellyfish1/jellyfish
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/share/
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/share/doc/jellyfish1/
-rw-r--r-- root/root 2333 2013-05-29 19:45 ./usr/share/doc/jellyfish1/README
-rw-r--r-- root/root 1220 2020-11-26 06:52 ./usr/share/doc/jellyfish1/changelog.Debian.gz
-rw-r--r-- root/root 2337 2020-11-26 06:52 ./usr/share/doc/jellyfish1/copyright
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/share/lintian/
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 66 2020-11-26 06:52 ./usr/share/lintian/overrides/jellyfish1
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/share/man/
drwxr-xr-x root/root 0 2020-11-26 06:52 ./usr/share/man/man1/
-rw-r--r-- root/root 4556 2020-11-26 06:52 ./usr/share/man/man1/jellyfish1.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 48784
Build-Time: 396
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 189
Job: jellyfish1_1.1.11-5
Machine Architecture: armhf
Package: jellyfish1
Package-Time: 619
Source-Version: 1.1.11-5
Space: 48784
Status: successful
Version: 1.1.11-5
--------------------------------------------------------------------------------
Finished at 2020-12-01T10:21:41Z
Build needed 00:10:19, 48784k disk space