jellyfish1 →
1.1.11-4 →
armhf → 2018-10-23 05:56:26
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| jellyfish1 1.1.11-4 (armhf) Tue, 23 Oct 2018 05:49:58 +0000 |
+==============================================================================+
Package: jellyfish1
Version: 1.1.11-4
Source Version: 1.1.11-4
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-6c406db6-3f2a-4d47-85ad-d1e61fac022e' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.9 MB]
Fetched 24.0 MB in 15s (1569 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 buster-staging/main jellyfish1 1.1.11-4 (dsc) [2009 B]
Get:2 http://172.17.0.1/private buster-staging/main jellyfish1 1.1.11-4 (tar) [1067 kB]
Get:3 http://172.17.0.1/private buster-staging/main jellyfish1 1.1.11-4 (diff) [4688 B]
Fetched 1074 kB in 1s (1671 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/jellyfish1-ZilCP5/jellyfish1-1.1.11' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/jellyfish1-ZilCP5' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-jzeVB8/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-jzeVB8/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-jzeVB8/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-jzeVB8/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-jzeVB8/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-jzeVB8/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-jzeVB8/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-jzeVB8/apt_archive ./ Packages [430 B]
Fetched 2106 B in 0s (10.3 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 28 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-jzeVB8/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15767 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~)
Filtered Build-Depends: debhelper (>= 11~)
dpkg-deb: building package 'sbuild-build-depends-jellyfish1-dummy' in '/<<BUILDDIR>>/resolver-jzeVB8/apt_archive/sbuild-build-depends-jellyfish1-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-jellyfish1-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-jzeVB8/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-jzeVB8/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-jzeVB8/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-jzeVB8/apt_archive ./ Sources [492 B]
Get:5 copy:/<<BUILDDIR>>/resolver-jzeVB8/apt_archive ./ Packages [571 B]
Fetched 2396 B in 0s (10.7 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install jellyfish1 build dependencies (apt-based resolver)
----------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libelf1
libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3
libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc libmagic1 libpipeline1
libsigsegv2 libtool libxml2 m4 man-db po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation 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 bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libelf1
libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3
libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc libmagic1 libpipeline1
libsigsegv2 libtool libxml2 m4 man-db po-debconf
sbuild-build-depends-jellyfish1-dummy
0 upgraded, 35 newly installed, 0 to remove and 28 not upgraded.
Need to get 10.2 MB/19.2 MB of archives.
After this operation, 67.0 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-jzeVB8/apt_archive ./ sbuild-build-depends-jellyfish1-dummy 0.invalid.0 [856 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-2+b1 [1160 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-8 [117 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-1.1 [771 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-8 [434 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.043-2 [20.2 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.043-2 [12.2 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.9.0-1+rpi1 [877 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-8 [1220 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.4.1 [989 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 10.2 MB in 5s (1912 kB/s)
Selecting previously unselected package libbsd0:armhf.
(Reading database ... 15767 files and directories currently installed.)
Preparing to unpack .../00-libbsd0_0.9.1-1_armhf.deb ...
Unpacking libbsd0:armhf (0.9.1-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../01-bsdmainutils_11.1.2_armhf.deb ...
Unpacking bsdmainutils (11.1.2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../02-groff-base_1.22.3-10_armhf.deb ...
Unpacking groff-base (1.22.3-10) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../03-libpipeline1_1.5.0-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.0-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../04-man-db_2.8.4-2+b1_armhf.deb ...
Unpacking man-db (2.8.4-2+b1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../05-libmagic-mgc_1%3a5.34-2_armhf.deb ...
Unpacking libmagic-mgc (1:5.34-2) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../06-libmagic1_1%3a5.34-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.34-2) ...
Selecting previously unselected package file.
Preparing to unpack .../07-file_1%3a5.34-2_armhf.deb ...
Unpacking file (1:5.34-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../08-gettext-base_0.19.8.1-8_armhf.deb ...
Unpacking gettext-base (0.19.8.1-8) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../09-libsigsegv2_2.12-2_armhf.deb ...
Unpacking libsigsegv2:armhf (2.12-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.18-1_armhf.deb ...
Unpacking m4 (1.4.18-1) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.69-11_all.deb ...
Unpacking autoconf (2.69-11) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20180224.1_all.deb ...
Unpacking autotools-dev (20180224.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.1-1.1_all.deb ...
Unpacking automake (1:1.16.1-1.1) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.19.8.1-8_all.deb ...
Unpacking autopoint (0.19.8.1-8) ...
Selecting previously unselected package libtool.
Preparing to unpack .../15-libtool_2.4.6-6_all.deb ...
Unpacking libtool (2.4.6-6) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../16-dh-autoreconf_19_all.deb ...
Unpacking dh-autoreconf (19) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../17-libarchive-zip-perl_1.64-1_all.deb ...
Unpacking libarchive-zip-perl (1.64-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../18-libfile-stripnondeterminism-perl_0.043-2_all.deb ...
Unpacking libfile-stripnondeterminism-perl (0.043-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../19-dh-strip-nondeterminism_0.043-2_all.deb ...
Unpacking dh-strip-nondeterminism (0.043-2) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../20-libelf1_0.170-0.5_armhf.deb ...
Unpacking libelf1:armhf (0.170-0.5) ...
Selecting previously unselected package dwz.
Preparing to unpack .../21-dwz_0.12-2_armhf.deb ...
Unpacking dwz (0.12-2) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../22-libglib2.0-0_2.58.1-2_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.58.1-2) ...
Selecting previously unselected package libfreetype6:armhf.
Preparing to unpack .../23-libfreetype6_2.8.1-2_armhf.deb ...
Unpacking libfreetype6:armhf (2.8.1-2) ...
Selecting previously unselected package libgraphite2-3:armhf.
Preparing to unpack .../24-libgraphite2-3_1.3.12-1_armhf.deb ...
Unpacking libgraphite2-3:armhf (1.3.12-1) ...
Selecting previously unselected package libharfbuzz0b:armhf.
Preparing to unpack .../25-libharfbuzz0b_1.9.0-1+rpi1_armhf.deb ...
Unpacking libharfbuzz0b:armhf (1.9.0-1+rpi1) ...
Selecting previously unselected package libicu-le-hb0:armhf.
Preparing to unpack .../26-libicu-le-hb0_1.0.3+git161113-5_armhf.deb ...
Unpacking libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Selecting previously unselected package libicu60:armhf.
Preparing to unpack .../27-libicu60_60.2-6_armhf.deb ...
Unpacking libicu60:armhf (60.2-6) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../28-libxml2_2.9.4+dfsg1-7_armhf.deb ...
Unpacking libxml2:armhf (2.9.4+dfsg1-7) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../29-libcroco3_0.6.12-2_armhf.deb ...
Unpacking libcroco3:armhf (0.6.12-2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../30-gettext_0.19.8.1-8_armhf.deb ...
Unpacking gettext (0.19.8.1-8) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../31-intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../32-po-debconf_1.0.20_all.deb ...
Unpacking po-debconf (1.0.20) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../33-debhelper_11.4.1_all.deb ...
Unpacking debhelper (11.4.1) ...
Selecting previously unselected package sbuild-build-depends-jellyfish1-dummy.
Preparing to unpack .../34-sbuild-build-depends-jellyfish1-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-jellyfish1-dummy (0.invalid.0) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libelf1:armhf (0.170-0.5) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.58.1-2) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-8) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libfreetype6:armhf (2.8.1-2) ...
Setting up libmagic-mgc (1:5.34-2) ...
Setting up libmagic1:armhf (1:5.34-2) ...
Setting up libgraphite2-3:armhf (1.3.12-1) ...
Processing triggers for libc-bin (2.27-6+rpi1) ...
Setting up dwz (0.12-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up autopoint (0.19.8.1-8) ...
Setting up libfile-stripnondeterminism-perl (0.043-2) ...
Setting up libharfbuzz0b:armhf (1.9.0-1+rpi1) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.34-2) ...
Setting up automake (1:1.16.1-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.4-2+b1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-6) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up dh-strip-nondeterminism (0.043-2) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up gettext (0.19.8.1-8) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.20) ...
Setting up debhelper (11.4.1) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-jellyfish1-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-6+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-6+rpi1 dpkg-dev_1.19.0.5 g++-8_8.2.0-7+rpi1 gcc-8_8.2.0-7+rpi1 libc6-dev_2.27-6+rpi1 libstdc++-8-dev_8.2.0-7+rpi1 libstdc++6_8.2.0-7+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.118 apt_1.7.0 autoconf_2.69-11 automake_1:1.16.1-1.1 autopoint_0.19.8.1-8 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-6+rpi1 binutils-arm-linux-gnueabihf_2.31.1-6+rpi1 binutils-common_2.31.1-6+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.2.0-7+rpi1 dash_0.5.10.2-1 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.4.1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.043-2 diffutils_1:3.6-1 dirmngr_2.2.10-3+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 e2fsprogs-l10n_1.44.4-2 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20180808-2 g++_4:8.1.0-1+rpi1 g++-8_8.2.0-7+rpi1 gcc_4:8.1.0-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-7+rpi1 gcc-8-base_8.2.0-7+rpi1 gettext_0.19.8.1-8 gettext-base_0.19.8.1-8 gnupg_2.2.10-3+rpi1 gnupg-agent_2.2.10-3+rpi1 gnupg-l10n_2.2.10-3+rpi1 gnupg-utils_2.2.10-3+rpi1 gpg_2.2.10-3+rpi1 gpg-agent_2.2.10-3+rpi1 gpg-wks-client_2.2.10-3+rpi1 gpg-wks-server_2.2.10-3+rpi1 gpgconf_2.2.10-3+rpi1 gpgsm_2.2.10-3+rpi1 gpgv_2.2.10-3+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2.1 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.54 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 krb5-locales_1.16.1-1 libacl1_2.2.52-3 libapparmor1_2.13-8 libapt-pkg5.0_1.7.0 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-7+rpi1 libassuan0_2.5.1-2 libatomic1_8.2.0-7+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbinutils_2.31.1-6+rpi1 libblkid1_2.32.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.27-6+rpi1 libc-dev-bin_2.27-6+rpi1 libc6_2.27-6+rpi1 libc6-dev_2.27-6+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-7+rpi1 libcom-err2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.10-1 libdebconfclient0_0.245 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.94-1+rpi1 libdrm2_2.4.94-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.6-1 libext2fs2_1.44.4-2 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.043-2 libfreetype6_2.8.1-2 libgcc-8-dev_8.2.0-7+rpi1 libgcc1_1:8.2.0-7+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.18-2 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgdbm6_1.18-2 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.2.0-7+rpi1 libgpg-error0_1.32-1 libgraphite2-3_1.3.12-1 libgssapi-krb5-2_1.16.1-1 libharfbuzz0b_1.9.0-1+rpi1 libhogweed4_3.4-1 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.6.2-1.1 libisl19_0.20-2 libjson-c3_0.12.1-1.3 libk5crypto3_1.16.1-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-1 libkrb5-3_1.16.1-1 libkrb5support0_1.16.1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnpth0_1.6-1 libnss-systemd_239-10+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_239-10+rpi1 libpam0g_1.1.8-3.8 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libreadline7_7.0-5 libsasl2-2_2.1.27~rc8-1 libsasl2-modules_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.25.2-1 libss2_1.44.4-2 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.2.0-7+rpi1 libstdc++6_8.2.0-7+rpi1 libsystemd0_239-10+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20180714-1 libtool_2.4.6-6 libubsan1_8.2.0-7+rpi1 libudev1_239-10+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32.1-0.1 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.5+dfsg-1+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.4-2+b1 mawk_1.3.3-17 mount_2.32.1-0.1 multiarch-support_2.27-6+rpi1 nano_3.1-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-7 pinentry-curses_1.1.0-1 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-jellyfish1-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_239-10+rpi1 systemd-sysv_239-10+rpi1 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_239-10+rpi1 util-linux_2.32.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Oct 18 06:05:05 2018 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_1.1.11-4.dsc
dpkg-source: info: extracting jellyfish1 in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking jellyfish1_1.1.11.orig.tar.gz
dpkg-source: info: unpacking jellyfish1_1.1.11-4.debian.tar.xz
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
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-6c406db6-3f2a-4d47-85ad-d1e61fac022e
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package jellyfish1
dpkg-buildpackage: info: source version 1.1.11-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build jellyfish1-1.1.11
dpkg-buildpackage: info: host architecture armhf
fakeroot 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 build-arch
dh build-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-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
configure: WARNING: unrecognized options: --disable-maintainer-mode
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... mt
checking if mt 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
configure: WARNING: unrecognized options: --disable-maintainer-mode
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/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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/stats_main.cc:26:
./jellyfish/square_binary_matrix.hpp: In static member function 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array<long long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/square_binary_matrix.hpp:64:112: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) {
^
In file included from jellyfish/stats_main.cc:25:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/stats_main.cc:26:
./jellyfish/square_binary_matrix.hpp:64:112: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) {
^
In file included from jellyfish/stats_main.cc:25:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
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/hash_merge.o jellyfish/hash_merge.cc
In file included from jellyfish/hash_merge.cc:32:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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]
memset(&head, '\0', sizeof(head));
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./jellyfish/compacted_hash.hpp:36:12: note: 'struct jellyfish::compacted_hash::header' declared here
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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/hash_merge.cc:34:
./jellyfish/square_binary_matrix.hpp: In function 'int merge_main(int, char**)':
./jellyfish/square_binary_matrix.hpp:138:19: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
if(columns[i] != other.columns[i])
~~~~~~~~~^
In file included from jellyfish/hash_merge.cc:33:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/hash_merge.cc:34:
./jellyfish/square_binary_matrix.hpp:87:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
free(columns);
~~~~^~~~~~~~~
In file included from jellyfish/hash_merge.cc:33:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
./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/mer_counter.o jellyfish/mer_counter.cc
In file included from jellyfish/mer_counter.cc:33:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:101:5: 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]
memset(&head, '\0', sizeof(head));
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./jellyfish/compacted_hash.hpp:36:12: note: 'struct jellyfish::compacted_hash::header' declared here
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:116:5: 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]
memset(&head, '\0', sizeof(head));
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./jellyfish/compacted_hash.hpp:36:12: note: 'struct jellyfish::compacted_hash::header' declared here
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:114:7: 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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:114:7: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:114:7: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/mer_counter.cc:38:
./jellyfish/square_binary_matrix.hpp: In member function 'void jellyfish::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/square_binary_matrix.hpp:61:82: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) {
^
In file included from jellyfish/mer_counter.cc:36:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
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]
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/mer_counter.cc:38:
./jellyfish/square_binary_matrix.hpp: In constructor 'jellyfish::invertible_hash::array<word, atomic_t, mem_block_t>::array(size_t, uint_t, uint_t, uint_t, size_t*) [with word = long long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]':
./jellyfish/square_binary_matrix.hpp:61:82: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) {
^
In file included from jellyfish/mer_counter.cc:36:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
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/histo_main.o jellyfish/histo_main.cc
In file included from jellyfish/histo_main.cc:25:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/histo_main.cc:27:
./jellyfish/square_binary_matrix.hpp: In static member function 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array<long long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/square_binary_matrix.hpp:64:112: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) {
^
In file included from jellyfish/histo_main.cc:26:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/histo_main.cc:27:
./jellyfish/square_binary_matrix.hpp:64:112: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) {
^
In file included from jellyfish/histo_main.cc:26:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
./jellyfish/misc.hpp: In function 'int histo_main(int, char**)':
./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
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=]
} 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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/dump_main.cc:26:
./jellyfish/square_binary_matrix.hpp: In static member function 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array<long long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/square_binary_matrix.hpp:64:112: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) {
^
In file included from jellyfish/dump_main.cc:25:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/dump_main.cc:26:
./jellyfish/square_binary_matrix.hpp:64:112: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) {
^
In file included from jellyfish/dump_main.cc:25:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
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/query_main.o jellyfish/query_main.cc
In file included from ./jellyfish/mapped_file.hpp:29,
from ./jellyfish/hash.hpp:27,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/query_main.cc:24:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/query_main.cc:24:
./jellyfish/square_binary_matrix.hpp: In static member function 'static jellyfish::raw_hash::query<_storage_t>::storage_t* jellyfish::raw_hash::query<_storage_t>::init(mapped_file&, SquareBinaryMatrix&, SquareBinaryMatrix&) [with _storage_t = jellyfish::invertible_hash::array<long long unsigned int, atomic::gcc, allocators::mmap>]':
./jellyfish/square_binary_matrix.hpp:64:112: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) {
^
In file included from jellyfish/query_main.cc:23:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/query_main.cc:24:
./jellyfish/square_binary_matrix.hpp:64:112: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) {
^
In file included from jellyfish/query_main.cc:23:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
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/dump_fastq_main.o jellyfish/dump_fastq_main.cc
In file included from jellyfish/dump_fastq_main.cc:25:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/dump_fastq_main.cc:27:
./jellyfish/square_binary_matrix.hpp: In static member function 'static storage_t* jellyfish::fastq_hash::raw_dumper<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]':
./jellyfish/square_binary_matrix.hpp:64:112: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) {
^
In file included from jellyfish/dump_fastq_main.cc:26:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/dump_fastq_main.cc:27:
./jellyfish/square_binary_matrix.hpp:64:112: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) {
^
In file included from jellyfish/dump_fastq_main.cc:26:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
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/histo_fastq_main.o jellyfish/histo_fastq_main.cc
In file included from jellyfish/histo_fastq_main.cc:26:
./jellyfish/err.hpp: In instantiation of 'err::raise_t<err_t>::~raise_t() [with err_t = mapped_file::ErrorMMap]':
./jellyfish/mapped_file.hpp:46:7: required from here
./jellyfish/err.hpp:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/histo_fastq_main.cc:28:
./jellyfish/square_binary_matrix.hpp: In static member function 'static storage_t* jellyfish::fastq_hash::raw_dumper<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]':
./jellyfish/square_binary_matrix.hpp:64:112: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) {
^
In file included from jellyfish/histo_fastq_main.cc:27:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/histo_fastq_main.cc:28:
./jellyfish/square_binary_matrix.hpp:64:112: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) {
^
In file included from jellyfish/histo_fastq_main.cc:27:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
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/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/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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/hash_fastq_merge.cc:19:
./jellyfish/square_binary_matrix.hpp: In static member function 'static storage_t* jellyfish::fastq_hash::raw_dumper<storage_t>::read(const mapped_file&) [with storage_t = jellyfish::aligned_values::array<long long unsigned int, jellyfish::Float, atomic::gcc, allocators::mmap>]':
./jellyfish/square_binary_matrix.hpp:64:112: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) {
^
In file included from jellyfish/hash_fastq_merge.cc:18:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/hash_fastq_merge.cc:19:
./jellyfish/square_binary_matrix.hpp:64:112: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
SquareBinaryMatrix(const SquareBinaryMatrix &rhs) : columns(first_alloc(rhs.get_size())), size(rhs.get_size()) {
^
In file included from jellyfish/hash_fastq_merge.cc:18:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from ./jellyfish/hash.hpp:31,
from ./jellyfish/mer_counting.hpp:28,
from jellyfish/hash_fastq_merge.cc:19:
./jellyfish/square_binary_matrix.hpp: In function 'int hash_fastq_merge_main(int, char**)':
./jellyfish/square_binary_matrix.hpp:61:82: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) {
^
In file included from jellyfish/hash_fastq_merge.cc:18:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
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/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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept
In file included from jellyfish/square_binary_matrix.cc:21:
./jellyfish/square_binary_matrix.hpp: In member function 'SquareBinaryMatrix SquareBinaryMatrix::transpose() const':
./jellyfish/square_binary_matrix.hpp:61:82: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) {
^
In file included from jellyfish/square_binary_matrix.cc:20:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from jellyfish/square_binary_matrix.cc:21:
./jellyfish/square_binary_matrix.hpp: In member function 'void SquareBinaryMatrix::load(std::istream*)':
./jellyfish/square_binary_matrix.hpp:55:13: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
columns = first_alloc(size);
~~~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from jellyfish/square_binary_matrix.cc:20:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from jellyfish/square_binary_matrix.cc:21:
./jellyfish/square_binary_matrix.hpp: In member function 'size_t SquareBinaryMatrix::read(const char*)':
./jellyfish/square_binary_matrix.hpp:55:13: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
columns = first_alloc(size);
~~~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from jellyfish/square_binary_matrix.cc:20:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from jellyfish/square_binary_matrix.cc:21:
./jellyfish/square_binary_matrix.hpp: In member function 'SquareBinaryMatrix SquareBinaryMatrix::operator*(const SquareBinaryMatrix&) const':
./jellyfish/square_binary_matrix.hpp:61:82: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) {
^
In file included from jellyfish/square_binary_matrix.cc:20:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from jellyfish/square_binary_matrix.cc:21:
./jellyfish/square_binary_matrix.hpp: In member function 'SquareBinaryMatrix SquareBinaryMatrix::inverse() const':
./jellyfish/square_binary_matrix.hpp:61:82: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) {
^
In file included from jellyfish/square_binary_matrix.cc:20:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
./jellyfish/misc.hpp:106:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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
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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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/8/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/8/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/8 -L/usr/lib/gcc/arm-linux-gnueabihf/8/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/8/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/arm-linux-gnueabihf/8/crtendS.o /usr/lib/gcc/arm-linux-gnueabihf/8/../../../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 cru .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
ar: `u' modifier ignored since `D' is the default (see `U')
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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: note: in C++11 destructors default to noexcept
In file included from /usr/include/c++/8/vector:69,
from jellyfish/generate_sequence.cc:18:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void generate_sequence_args::parse(int, char**)':
/usr/include/c++/8/bits/vector.tcc:109:4: 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
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from jellyfish/generate_sequence.cc:23:
./jellyfish/misc.hpp: In function 'int main(int, char**)':
./jellyfish/misc.hpp:106:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
Tptr<T> ptr;
^~~
In file included from jellyfish/generate_sequence.cc:24:
./jellyfish/square_binary_matrix.hpp:87:11: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
free(columns);
~~~~^~~~~~~~~
In file included from jellyfish/generate_sequence.cc:23:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from jellyfish/generate_sequence.cc:24:
./jellyfish/square_binary_matrix.hpp:61:82: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) {
^
In file included from jellyfish/generate_sequence.cc:23:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
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/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=]
} 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:123:39: warning: throw will always call terminate() [-Wterminate]
~raise_t() { throw err_t(oss.str()); }
^
./jellyfish/err.hpp:123:39: 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:123:39: warning: throw will always call terminate() [-Wterminate]
./jellyfish/err.hpp:123:39: 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:61:82: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) {
^
In file included from ./jellyfish/square_binary_matrix.hpp:28,
from unit_tests/test_square_binary_matrix.cc:3:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
./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]
In file included from unit_tests/test_square_binary_matrix.cc:3:
./jellyfish/square_binary_matrix.hpp:61:82: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) {
^
In file included from ./jellyfish/square_binary_matrix.hpp:28,
from unit_tests/test_square_binary_matrix.cc:3:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from unit_tests/test_square_binary_matrix.cc:3:
./jellyfish/square_binary_matrix.hpp:61:82: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) {
^
In file included from ./jellyfish/square_binary_matrix.hpp:28,
from unit_tests/test_square_binary_matrix.cc:3:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
In file included from unit_tests/test_square_binary_matrix.cc:3:
./jellyfish/square_binary_matrix.hpp:61:82: warning: 'ptr' may be used uninitialized in this function [-Wmaybe-uninitialized]
explicit SquareBinaryMatrix(int _size) :columns(first_alloc(_size)), size(_size) {
^
In file included from ./jellyfish/square_binary_matrix.hpp:28,
from unit_tests/test_square_binary_matrix.cc:3:
./jellyfish/misc.hpp:106:11: note: 'ptr' was declared here
Tptr<T> ptr;
^~~
g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I./unit_tests/gtest -I./unit_tests/gtest/include -g -O2 -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
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
fakeroot debian/rules binary-arch
dh binary-arch
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
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_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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
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 __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_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
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'jellyfish1' in '../jellyfish1_1.1.11-4_armhf.deb'.
dpkg-deb: building package 'jellyfish1-dbgsym' in '../jellyfish1-dbgsym_1.1.11-4_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../jellyfish1_1.1.11-4_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build jellyfish1-1.1.11
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-10-23T05:56:23Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
jellyfish1_1.1.11-4_armhf.changes:
----------------------------------
Format: 1.8
Date: Thu, 18 Oct 2018 08:03:17 +0200
Source: jellyfish1
Binary: jellyfish1
Architecture: armhf
Version: 1.1.11-4
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
jellyfish1 - count k-mers in DNA sequences
Changes:
jellyfish1 (1.1.11-4) unstable; urgency=medium
.
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
Checksums-Sha1:
4ad1a563a9d7a0d0d209b7e84942e40045451769 1581392 jellyfish1-dbgsym_1.1.11-4_armhf.deb
3eb939546eb157c48b0cf0c19b95e0f8b6702ed1 4635 jellyfish1_1.1.11-4_armhf.buildinfo
3e24f6afd332f0061b87e2daaa36435c440f4334 133480 jellyfish1_1.1.11-4_armhf.deb
Checksums-Sha256:
6c531fabae1f4b72401501cba1abef3310aa493d5b1a8362e3d82d9ff43dae45 1581392 jellyfish1-dbgsym_1.1.11-4_armhf.deb
146d45d65ebbb0d1eac557efe9b551105fdd6a3c4ab3f206037903ce0f9efb6b 4635 jellyfish1_1.1.11-4_armhf.buildinfo
a23c1e5abc49ec740aa571f9b4dc072f34a6cc3763ff21c8b3efc5074f044b43 133480 jellyfish1_1.1.11-4_armhf.deb
Files:
b6fcab54e82c1a5c3a4d5a2840b6e11c 1581392 debug optional jellyfish1-dbgsym_1.1.11-4_armhf.deb
3c18d31a057f80db34be003011551e33 4635 science optional jellyfish1_1.1.11-4_armhf.buildinfo
a05fb09d2563ec19fd1bc89092440f05 133480 science optional jellyfish1_1.1.11-4_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
jellyfish1-dbgsym_1.1.11-4_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 1581392 bytes: control archive=600 bytes.
426 bytes, 12 lines control
212 bytes, 2 lines md5sums
Package: jellyfish1-dbgsym
Source: jellyfish1
Version: 1.1.11-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1660
Depends: jellyfish1 (= 1.1.11-4)
Section: debug
Priority: optional
Description: debug symbols for jellyfish1
Build-Ids: 47ca71db4140bc163755bbfc87f4e33d486ea167 8d605e842f36aede720309f98174d61bedb3851d
drwxr-xr-x root/root 0 2018-10-18 06:03 ./
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/lib/debug/.build-id/47/
-rw-r--r-- root/root 458360 2018-10-18 06:03 ./usr/lib/debug/.build-id/47/ca71db4140bc163755bbfc87f4e33d486ea167.debug
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/lib/debug/.build-id/8d/
-rw-r--r-- root/root 1229172 2018-10-18 06:03 ./usr/lib/debug/.build-id/8d/605e842f36aede720309f98174d61bedb3851d.debug
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-10-18 06:03 ./usr/share/doc/jellyfish1-dbgsym -> jellyfish1
jellyfish1_1.1.11-4_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 133480 bytes: control archive=1344 bytes.
1309 bytes, 28 lines control
507 bytes, 7 lines md5sums
30 bytes, 1 lines shlibs
67 bytes, 2 lines triggers
Package: jellyfish1
Version: 1.1.11-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 599
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2)
Enhances: kraken
Section: science
Priority: optional
Homepage: http://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 2018-10-18 06:03 ./
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/bin/
lrwxrwxrwx root/root 0 2018-10-18 06:03 ./usr/bin/jellyfish1 -> ../lib/jellyfish1/jellyfish
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2018-10-18 06:03 ./usr/lib/arm-linux-gnueabihf/libjellyfish-1.1.so.1 -> libjellyfish-1.1.so.1.0.1
-rw-r--r-- root/root 350632 2018-10-18 06:03 ./usr/lib/arm-linux-gnueabihf/libjellyfish-1.1.so.1.0.1
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/lib/jellyfish1/
-rwxr-xr-x root/root 228920 2018-10-18 06:03 ./usr/lib/jellyfish1/jellyfish
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-10-18 06:03 ./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 1069 2018-10-18 06:03 ./usr/share/doc/jellyfish1/changelog.Debian.gz
-rw-r--r-- root/root 2337 2018-10-18 06:03 ./usr/share/doc/jellyfish1/copyright
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/lintian/
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 66 2018-10-18 06:03 ./usr/share/lintian/overrides/jellyfish1
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/man/
drwxr-xr-x root/root 0 2018-10-18 06:03 ./usr/share/man/man1/
-rw-r--r-- root/root 4556 2018-10-18 06:03 ./usr/share/man/man1/jellyfish1.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 52444
Build-Time: 247
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 115
Job: jellyfish1_1.1.11-4
Machine Architecture: armhf
Package: jellyfish1
Package-Time: 385
Source-Version: 1.1.11-4
Space: 52444
Status: successful
Version: 1.1.11-4
--------------------------------------------------------------------------------
Finished at 2018-10-23T05:56:23Z
Build needed 00:06:25, 52444k disk space