crac →
2.5.2+dfsg-2 →
armhf → 2020-12-14 13:47:35
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| crac 2.5.2+dfsg-2 (armhf) Mon, 14 Dec 2020 13:35:48 +0000 |
+==============================================================================+
Package: crac
Version: 2.5.2+dfsg-2
Source Version: 2.5.2+dfsg-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-1b3a284e-b48b-44f8-a0e7-7ec2e17a0d99' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [12.0 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.0 MB]
Fetched 24.9 MB in 25s (999 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: 'crac' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/crac.git
Please use:
git clone https://salsa.debian.org/med-team/crac.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 674 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main crac 2.5.2+dfsg-2 (dsc) [2046 B]
Get:2 http://172.17.0.1/private bullseye-staging/main crac 2.5.2+dfsg-2 (tar) [658 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main crac 2.5.2+dfsg-2 (diff) [13.3 kB]
Fetched 674 kB in 0s (3142 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/crac-C8ocm0/crac-2.5.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/crac-C8ocm0' 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-Vwbw0U/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-Vwbw0U/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-Vwbw0U/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-Vwbw0U/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Vwbw0U/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Vwbw0U/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Vwbw0U/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Vwbw0U/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2624 B/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:
bsdextrautils krb5-locales libnss-nis libnss-nisplus netbase sensible-utils
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 5 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-Vwbw0U/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 (23.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12757 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-compat (= 12), zlib1g-dev, libhts-dev, libjellyfish-2.0-dev, libgzstream-dev, libgkarrays-dev, pkg-config, rsync
Filtered Build-Depends: debhelper-compat (= 12), zlib1g-dev, libhts-dev, libjellyfish-2.0-dev, libgzstream-dev, libgkarrays-dev, pkg-config, rsync
dpkg-deb: building package 'sbuild-build-depends-crac-dummy' in '/<<BUILDDIR>>/resolver-Vwbw0U/apt_archive/sbuild-build-depends-crac-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-crac-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-Vwbw0U/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Vwbw0U/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Vwbw0U/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Vwbw0U/apt_archive ./ Sources [540 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Vwbw0U/apt_archive ./ Packages [622 B]
Fetched 2495 B in 1s (3079 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install crac 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:
krb5-locales libnss-nis libnss-nisplus netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbrotli1 libcroco3 libcurl3-gnutls
libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libgkarrays-dev libgkarrays1 libglib2.0-0
libgzstream-dev libgzstream0 libhts-dev libhts3 libicu67 libjellyfish-2.0-2
libjellyfish-2.0-dev liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpopt0 libpsl5 librtmp1 libsigsegv2 libssh2-1
libsub-override-perl libtool libuchardet0 libxml2 libxxhash0 m4 man-db
pkg-config po-debconf rsync zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev
libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev liblzma-doc
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl openssh-client openssh-server python3
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs publicsuffix libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbrotli1 libcroco3 libcurl3-gnutls
libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libgkarrays-dev libgkarrays1 libglib2.0-0
libgzstream-dev libgzstream0 libhts-dev libhts3 libicu67 libjellyfish-2.0-2
libjellyfish-2.0-dev liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpopt0 libpsl5 librtmp1 libsigsegv2 libssh2-1
libsub-override-perl libtool libuchardet0 libxml2 libxxhash0 m4 man-db
pkg-config po-debconf rsync sbuild-build-depends-crac-dummy zlib1g-dev
0 upgraded, 55 newly installed, 0 to remove and 5 not upgraded.
Need to get 25.8 MB of archives.
After this operation, 82.4 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Vwbw0U/apt_archive ./ sbuild-build-depends-crac-dummy 0.invalid.0 [912 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libpopt0 armhf 1.18-2 [46.8 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libxxhash0 armhf 0.8.0-1 [22.7 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf rsync armhf 3.2.3-2 [289 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3 [188 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-1 [162 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20201015-2 [162 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.3-2 [1178 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-5 [8288 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3 [1009 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.42.0-1 [66.7 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.9.0-1 [141 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.72.0-1 [297 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-gnutls-dev armhf 7.72.0-1 [371 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.6-1 [47.4 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libdeflate-dev armhf 1.6-1 [40.8 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libgkarrays1 armhf 2.1.0+dfsg-4 [52.9 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libgkarrays-dev armhf 2.1.0+dfsg-4 [80.7 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libgzstream0 armhf 1.5+dfsg-5 [6268 B]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libgzstream-dev armhf 1.5+dfsg-5 [6728 B]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.11-2 [318 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.11-2 [4495 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libjellyfish-2.0-2 armhf 2.3.0-8 [56.1 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libjellyfish-2.0-dev armhf 2.3.0-8 [129 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Preparing to unpack .../37-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:armhf.
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Unpacking libssh2-1:armhf (1.9.0-1) ...
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Unpacking libcurl3-gnutls:armhf (7.72.0-1) ...
Selecting previously unselected package libcurl4-gnutls-dev:armhf.
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Unpacking libcurl4-gnutls-dev:armhf (7.72.0-1) ...
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Unpacking libdeflate0:armhf (1.6-1) ...
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Unpacking libdeflate-dev:armhf (1.6-1) ...
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Unpacking libgkarrays-dev (2.1.0+dfsg-4) ...
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Unpacking libgzstream0 (1.5+dfsg-5) ...
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Unpacking libgzstream-dev (1.5+dfsg-5) ...
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Unpacking libhts3:armhf (1.11-2) ...
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Unpacking liblzma-dev:armhf (5.2.4-1) ...
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Unpacking libjellyfish-2.0-2:armhf (2.3.0-8) ...
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Unpacking pkg-config (0.29.2-1) ...
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Preparing to unpack .../54-sbuild-build-depends-crac-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-crac-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpsl5:armhf (0.21.0-1.1) ...
Setting up libgkarrays1 (2.1.0+dfsg-4) ...
Setting up libicu67:armhf (67.1-5) ...
Setting up libgkarrays-dev (2.1.0+dfsg-4) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.66.3-2) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.3) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libnghttp2-14:armhf (1.42.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up libdeflate0:armhf (1.6-1) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.39-3) ...
Setting up libjellyfish-2.0-2:armhf (2.3.0-8) ...
Setting up autotools-dev (20180224.1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up pkg-config (0.29.2-1) ...
Setting up libgzstream0 (1.5+dfsg-5) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libxxhash0:armhf (0.8.0-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.9.0-1) ...
Setting up libdeflate-dev:armhf (1.6-1) ...
Setting up libelf1:armhf (0.182-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.3) ...
Setting up libpopt0:armhf (1.18-2) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libjellyfish-2.0-dev:armhf (2.3.0-8) ...
Setting up libtool (2.4.6-14) ...
Setting up m4 (1.4.18-4) ...
Setting up libcurl3-gnutls:armhf (7.72.0-1) ...
Setting up libcurl4-gnutls-dev:armhf (7.72.0-1) ...
Setting up libgzstream-dev (1.5+dfsg-5) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13+20201015-2) ...
Setting up groff-base (1.22.4-5) ...
Setting up rsync (3.2.3-2) ...
invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of start.
Setting up automake (1:1.16.2-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libhts3:armhf (1.11-2) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libhts-dev:armhf (1.11-2) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.3) ...
Setting up sbuild-build-depends-crac-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-4+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-19+rpi1 gcc-10_10.2.0-19+rpi1 libc6-dev_2.31-5+rpi1 libstdc++-10-dev_10.2.0-19+rpi1 libstdc++6_10.2.0-19+rpi1 linux-libc-dev_5.9.6-1+rpi1+b1
Package versions: adduser_3.118 apt_2.1.12 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1~rc3-1 binutils_2.35.1-4+rpi1 binutils-arm-linux-gnueabihf_2.35.1-4+rpi1 binutils-common_2.35.1-4+rpi1 bsdextrautils_2.36.1-2 bsdutils_1:2.36.1-2 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.0-19+rpi1 dash_0.5.11+git20200708+dd9ef66-2 debconf_1.5.74 debhelper_13.3 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13+20201015-2 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1.1 fdisk_2.36.1-2 file_1:5.39-3 findutils_4.7.0+git20201010-2 g++_4:10.2.0-1+rpi1 g++-10_10.2.0-19+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.0-19+rpi1 gcc-10-base_10.2.0-19+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-5+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.59 intltool-debian_0.35.0+20060710.5 krb5-locales_1.18.3-4 libacl1_2.2.53-8 libapt-pkg6.0_2.1.12 libarchive-zip-perl_1.68-1 libasan6_10.2.0-19+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-19+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1+b1 libbinutils_2.35.1-4+rpi1 libblkid1_2.36.1-2 libboost-iostreams1.71.0_1.71.0-7+b1 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-5+rpi1 libc-dev-bin_2.31-5+rpi1 libc6_2.31-5+rpi1 libc6-dev_2.31-5+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.0-19+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-4+rpi1 libctf0_2.35.1-4+rpi1 libcurl3-gnutls_7.72.0-1 libcurl4-gnutls-dev_7.72.0-1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.255 libdebhelper-perl_13.3 libdeflate-dev_1.6-1 libdeflate0_1.6-1 libdpkg-perl_1.20.5+rpi1 libelf1_0.182-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1.1 libfdisk1_2.36.1-2 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-19+rpi1 libgcc-s1_10.2.0-19+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgkarrays-dev_2.1.0+dfsg-4 libgkarrays1_2.1.0+dfsg-4 libglib2.0-0_2.66.3-2 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.6.15-4 libgomp1_10.2.0-19+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libgzstream-dev_1.5+dfsg-5 libgzstream0_1.5+dfsg-5 libhogweed6_3.6-2 libhts-dev_1.11-2 libhts3_1.11-2 libicu67_67.1-5 libidn2-0_2.3.0-4 libisl23_0.23-1 libjellyfish-2.0-2_2.3.0-8 libjellyfish-2.0-dev_2.3.0-8 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-2 libldap-2.4-2_2.4.56+dfsg-1+rpi1+b1 libldap-common_2.4.56+dfsg-1+rpi1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-2 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-1 libnettle8_3.6-2 libnghttp2-14_1.42.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.21-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.35-2 libpcre3_2:8.39-13 libperl5.32_5.32.0-5 libpipeline1_1.5.3-1 libpopt0_1.18-2 libpsl5_0.21.0-1.1 libreadline8_8.1~rc3-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.0-3+rpi1 libselinux1_3.1-2+b1 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.4-2 libsigsegv2_2.12-2 libsmartcols1_2.36.1-2 libsqlite3-0_3.34.0-1 libss2_1.45.6-1 libssh2-1_1.9.0-1 libssl1.1_1.1.1h-1 libstdc++-10-dev_10.2.0-19+rpi1 libstdc++6_10.2.0-19+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.6-4+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-19+rpi1 libuchardet0_0.0.7-1 libudev1_246.6-4+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-2 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6.3 libxxhash0_0.8.0-1 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.9.6-1+rpi1+b1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36.1-2 ncurses-base_6.2+20201114-1 ncurses-bin_6.2+20201114-1 netbase_6.2 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.32.0-5 perl-base_5.32.0-5 perl-modules-5.32_5.32.0-5 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.1~rc3-1 rsync_3.2.3-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-crac-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2020d-1 util-linux_2.36.1-2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.bYPO74zs/trustedkeys.kbx': General error
gpgv: Signature made Fri Jul 26 20:44:09 2019 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 ./crac_2.5.2+dfsg-2.dsc
dpkg-source: info: extracting crac in /<<BUILDDIR>>/crac-2.5.2+dfsg
dpkg-source: info: unpacking crac_2.5.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking crac_2.5.2+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_debian_packaged_libgzstream.patch
dpkg-source: info: applying use_debian_packaged_libjellyfish.patch
dpkg-source: info: applying skip_failed_test_bug-14958.patch
dpkg-source: info: applying use_debian_packages_libgtarrays.patch
dpkg-source: info: applying reproducible_build.patch
dpkg-source: info: applying cross.patch
Check disc 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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-1b3a284e-b48b-44f8-a0e7-7ec2e17a0d99
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package crac
dpkg-buildpackage: info: source version 2.5.2+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
aclocal: warning: couldn't open directory 'config/m4': No such file or directory
libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'.
libtoolize: copying file 'config/ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'config/m4'.
libtoolize: copying file 'config/m4/libtool.m4'
libtoolize: copying file 'config/m4/ltoptions.m4'
libtoolize: copying file 'config/m4/ltsugar.m4'
libtoolize: copying file 'config/m4/ltversion.m4'
libtoolize: copying file 'config/m4/lt~obsolete.m4'
configure.ac:147: installing 'config/compile'
configure.ac:139: installing 'config/config.guess'
configure.ac:139: installing 'config/config.sub'
configure.ac:137: installing 'config/install-sh'
configure.ac:137: installing 'config/missing'
src/Makefile.am: installing 'config/depcomp'
test_f/Makefile.am:109: warning: shell find . -name "*.should_get": non-POSIX variable name
test_f/Makefile.am:109: (probably a GNU make extension)
test_f/Makefile.am:110: warning: shell find . -name "*.fasta" -o -name "*.fa": non-POSIX variable name
test_f/Makefile.am:110: (probably a GNU make extension)
test_f/Makefile.am:111: warning: shell find . -name "*.fastq" -o -name "*.fq": non-POSIX variable name
test_f/Makefile.am:111: (probably a GNU make extension)
parallel-tests: installing 'config/test-driver'
dh_auto_configure -a
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking 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 build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for gawk... (cached) mawk
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 whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
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... gcc -E
checking whether make sets $(MAKE)... (cached) yes
checking whether ln -s works... yes
checking how to print strings... printf
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 the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for ANSI C header files... no
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
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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
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checking whether to build static libraries... no
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
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checking for rpmbuild... no
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checking pkg-config is at least version 0.9.0... yes
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configure: creating ./config.status
config.status: creating control
config.status: creating crac.spec
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating scripts/Makefile
config.status: creating src/libReadsInfo/Makefile
config.status: creating src/libSSA/Makefile
config.status: creating src/libReadsReader/Makefile
config.status: creating src/libReadsReader/kseq/Makefile
config.status: creating man/Makefile
config.status: creating man/crac.1
config.status: creating scripts/crac-client
config.status: creating test_f/Makefile
config.status: creating test_f/bug/Makefile
config.status: creating test_f/causes/Makefile
config.status: creating test_f/cigar/Makefile
config.status: creating test_f/splices_adjust/Makefile
config.status: creating config/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
Making all in src
make[2]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src'
Making all in libReadsInfo
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsInfo'
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-BioTagIndelInfo.o `test -f 'BioTagIndelInfo.cpp' || echo './'`BioTagIndelInfo.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-BioUndeterminedInfo.o `test -f 'BioUndeterminedInfo.cpp' || echo './'`BioUndeterminedInfo.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-cigarTypes.o `test -f 'cigarTypes.cpp' || echo './'`cigarTypes.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-Cigar.o `test -f 'Cigar.cpp' || echo './'`Cigar.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-DuplicationInfo.o `test -f 'DuplicationInfo.cpp' || echo './'`DuplicationInfo.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-genericInfo.o `test -f 'genericInfo.cpp' || echo './'`genericInfo.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-IndelInfo.o `test -f 'IndelInfo.cpp' || echo './'`IndelInfo.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-repetitionInfo.o `test -f 'repetitionInfo.cpp' || echo './'`repetitionInfo.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SeqErrInfo.o `test -f 'SeqErrInfo.cpp' || echo './'`SeqErrInfo.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SNPInfo.o `test -f 'SNPInfo.cpp' || echo './'`SNPInfo.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceInfo.o `test -f 'SpliceInfo.cpp' || echo './'`SpliceInfo.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceInterInfo.o `test -f 'SpliceInterInfo.cpp' || echo './'`SpliceInterInfo.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceIntraInfo.o `test -f 'SpliceIntraInfo.cpp' || echo './'`SpliceIntraInfo.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SpliceNoCoverInfo.o `test -f 'SpliceNoCoverInfo.cpp' || echo './'`SpliceNoCoverInfo.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-SplicingInfo.o `test -f 'SplicingInfo.cpp' || echo './'`SplicingInfo.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-samLine.o `test -f 'samLine.cpp' || echo './'`samLine.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-samHeader.o `test -f 'samHeader.cpp' || echo './'`samHeader.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-bamUtils.o `test -f 'bamUtils.cpp' || echo './'`bamUtils.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-tagInfo.o `test -f 'tagInfo.cpp' || echo './'`tagInfo.cpp
samHeader.cpp: In member function 'bam_hdr_t* SamHeader::writeBamHeader(samFile*)':
samHeader.cpp:160:15: warning: ignoring return value of 'int sam_hdr_write(samFile*, const sam_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result]
160 | sam_hdr_write(out,h);
| ~~~~~~~~~~~~~^~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsInfo_a-undeterminedErrorInfo.o `test -f 'undeterminedErrorInfo.cpp' || echo './'`undeterminedErrorInfo.cpp
In file included from ../libReadsReader/readsReader.h:57,
from ../Read.h:55,
from ../ReadIndex.h:52,
from ../Support.h:59,
from tagInfo.h:71,
from tagInfo.cpp:53:
../libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
../libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
../libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT'
59 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/htslib/kstring.h:31,
from /usr/include/htslib/hts.h:37,
from /usr/include/htslib/sam.h:31,
from samLine.h:59,
from samLine.cpp:52:
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'OptionalField::OptionalField(const char*, char)' at samLine.cpp:60:10:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'OptionalField::OptionalField(const char*, char)' at samLine.cpp:60:10,
inlined from 'CharOptionalField::CharOptionalField(const char*, char)' at samLine.cpp:91:34:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'OptionalField::OptionalField(const char*, char)' at samLine.cpp:60:10,
inlined from 'IntOptionalField::IntOptionalField(const char*, int)' at samLine.cpp:117:34:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'OptionalField::OptionalField(const char*, char)' at samLine.cpp:60:10,
inlined from 'IntOptionalField::IntOptionalField(const char*, uint)' at samLine.cpp:121:34:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'OptionalField::OptionalField(const char*, char)' at samLine.cpp:60:10,
inlined from 'StringOptionalField::StringOptionalField(const char*, std::string)' at samLine.cpp:147:34:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'OptionalField::OptionalField(const char*, char)' at samLine.cpp:60:10,
inlined from 'StringOptionalField::StringOptionalField(const char*, char*)' at samLine.cpp:150:34:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'OptionalField::OptionalField(const char*, char)' at samLine.cpp:60:10,
inlined from 'CharOptionalField::CharOptionalField(const char*, char)' at samLine.cpp:91:34,
inlined from 'void SamLine::addOptionalField(const char*, char)' at samLine.cpp:476:68:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'OptionalField::OptionalField(const char*, char)' at samLine.cpp:60:10,
inlined from 'IntOptionalField::IntOptionalField(const char*, int)' at samLine.cpp:117:34,
inlined from 'void SamLine::addOptionalField(const char*, int)' at samLine.cpp:485:67:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'OptionalField::OptionalField(const char*, char)' at samLine.cpp:60:10,
inlined from 'IntOptionalField::IntOptionalField(const char*, uint)' at samLine.cpp:121:34,
inlined from 'void SamLine::addOptionalField(const char*, uint)' at samLine.cpp:494:67:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'OptionalField::OptionalField(const char*, char)' at samLine.cpp:60:10,
inlined from 'StringOptionalField::StringOptionalField(const char*, std::string)' at samLine.cpp:147:34,
inlined from 'void SamLine::addOptionalField(const char*, const string&)' at samLine.cpp:503:70:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'OptionalField::OptionalField(const char*, char)' at samLine.cpp:60:10,
inlined from 'StringOptionalField::StringOptionalField(const char*, std::string)' at samLine.cpp:147:34,
inlined from 'void SamLine::addOptionalField(const char*, const char*)' at samLine.cpp:512:70:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 2 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rm -f libReadsInfo.a
ar cru libReadsInfo.a libReadsInfo_a-BioTagIndelInfo.o libReadsInfo_a-BioUndeterminedInfo.o libReadsInfo_a-cigarTypes.o libReadsInfo_a-Cigar.o libReadsInfo_a-DuplicationInfo.o libReadsInfo_a-genericInfo.o libReadsInfo_a-IndelInfo.o libReadsInfo_a-repetitionInfo.o libReadsInfo_a-SeqErrInfo.o libReadsInfo_a-SNPInfo.o libReadsInfo_a-SpliceInfo.o libReadsInfo_a-SpliceInterInfo.o libReadsInfo_a-SpliceIntraInfo.o libReadsInfo_a-SpliceNoCoverInfo.o libReadsInfo_a-SplicingInfo.o libReadsInfo_a-samLine.o libReadsInfo_a-samHeader.o libReadsInfo_a-bamUtils.o libReadsInfo_a-tagInfo.o libReadsInfo_a-undeterminedErrorInfo.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libReadsInfo.a
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsInfo'
Making all in libSSA
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA'
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o cracIndex.o cracIndex.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bitarray.o bitarray.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bitrankw32int.o bitrankw32int.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o chrPosition.o chrPosition.cpp
cracIndex.cpp:85:30: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
85 | cerr << "\tCompiled on " <<__DATE__ << endl << endl;
| ^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o HuffAlphabetRank.o HuffAlphabetRank.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Huffman_Codes.o Huffman_Codes.cpp
In file included from ./seqan/basic.h:64,
from ./seqan/sequence.h:27,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10,
from cracIndex.cpp:67:
./seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
./seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
1001 | typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
| ^~~~~~~~~~~
./seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
./seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
1027 | typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
| ^~~~~~~~~~~
./seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
./seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
1051 | typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
| ^~~~~~~~~~
In file included from ./seqan/sequence.h:38,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10,
from cracIndex.cpp:67:
./seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
./seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
239 | typedef typename Value<TLeft>::Type TLeftValue;
| ^~~~~~~~~~
In file included from ./seqan/sequence.h:51,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10,
from cracIndex.cpp:67:
./seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
./seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
811 | typedef String<TTargetValue, TTargetSpec> TTarget;
| ^~~~~~~
./seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
./seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
821 | typedef String<TTargetValue, TTargetSpec> TTarget;
| ^~~~~~~
./seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
./seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
834 | typedef String<TTargetValue, TTargetSpec> TTarget;
| ^~~~~~~
./seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
./seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
844 | typedef String<TTargetValue, TTargetSpec> TTarget;
| ^~~~~~~
./seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
./seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
1044 | typedef String<TTargetValue, TTargetSpec> TTarget;
| ^~~~~~~
./seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
./seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
1056 | typedef String<TTargetValue, TTargetSpec> TTarget;
| ^~~~~~~
./seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
./seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
1070 | typedef String<TTargetValue, TTargetSpec> TTarget;
| ^~~~~~~
./seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
./seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
1082 | typedef String<TTargetValue, TTargetSpec> TTarget;
| ^~~~~~~
./seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
./seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
1249 | typedef String<TTargetValue, TTargetSpec> TTarget;
| ^~~~~~~
./seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
./seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
1263 | typedef String<TTargetValue, TTargetSpec> TTarget;
| ^~~~~~~
./seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
./seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
1279 | typedef String<TTargetValue, TTargetSpec> TTarget;
| ^~~~~~~
./seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
./seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
1293 | typedef String<TTargetValue, TTargetSpec> TTarget;
| ^~~~~~~
In file included from ./seqan/sequence.h:53,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10,
from cracIndex.cpp:67:
./seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
./seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
456 | typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
| ^~~~~
In file included from ./seqan/sequence.h:57,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10,
from cracIndex.cpp:67:
./seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
./seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
594 | typedef typename Iterator<T, Standard>::Type TIterator;
| ^~~~~~~~~
./seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
./seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
758 | typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
| ^~~~~
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateOnGenome.o locateOnGenome.cpp
In file included from ./seqan/sequence.h:62,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10,
from cracIndex.cpp:67:
./seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
./seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
1647 | typedef typename Id<TStringSet>::Type TId;
| ^~~
In file included from ./seqan/index.h:82,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:11,
from cracIndex.cpp:67:
./seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0> >&, TIter)':
./seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
273 | typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
| ^~~~~~~
./seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
./seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
309 | typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
| ^~~~~~~
./seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
310 | typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
| ^~~~~
./seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
./seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
322 | typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
| ^~~~~~~
./seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
./seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
424 | typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
| ^~~~~~~
./seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
./seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
492 | typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
| ^~~~~~~
In file included from ./seqan/index.h:83,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:11,
from cracIndex.cpp:67:
./seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
./seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
370 | typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
| ^~~~~~~
./seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
./seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
387 | typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
| ^~~~~~~
./seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
./seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
415 | typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
| ^~~~~~~
In file included from ./seqan/file.h:66,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/multikey_qsort.h:6,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:8,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:13,
from cracIndex.cpp:67:
./seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
./seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
138 | typedef typename Row<TAlign>::Type TRow;
| ^~~~
./seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
./seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
252 | typedef typename Position<TAlign>::Type TPosition;
| ^~~~~~~~~
In file included from ./seqan/file.h:69,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/multikey_qsort.h:6,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:8,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:13,
from cracIndex.cpp:67:
./seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
./seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
66 | typedef typename Row<TAlign>::Type TRow;
| ^~~~
In file included from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:13,
from cracIndex.cpp:67:
/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:156:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
156 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:156:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
156 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:157:6: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
157 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/diff_sample.h:157:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
157 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from cracIndex.cpp:67:
/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In destructor 'KarkkainenBlockwiseSA<TStr>::~KarkkainenBlockwiseSA()':
/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:206:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
206 | if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
| ^~
/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:206:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
206 | if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
| ^~~
/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
380 | typedef typename Value<TStr>::Type TAlphabet;
| ^~~~~~~~~
/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:745:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
745 | typedef typename Value<TStr>::Type TAlphabet;
| ^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateTags.o locateTags.cpp
In file included from ./seqan/sequence.h:57,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10,
from cracIndex.cpp:67:
./seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
./seqan/sequence/string_packed.h:906:72: required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = unsigned int]'
./seqan/sequence/string_packed.h:1237:17: required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = int]'
./seqan/sequence/string_base.h:181:29: required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = unsigned int]'
/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:354:32: required from here
./seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<unnamed>' and 'enum seqan::BitsPerValue<unsigned int>::<unnamed>' [-Wenum-compare]
294 | VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
./seqan/sequence/string_packed.h:294:37: warning: comparison between types 'seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<unnamed enum>' and 'seqan::BitsPerValue<unsigned int>::<unnamed enum>' [-Wsign-compare]
./seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
./seqan/sequence/string_packed.h:958:79: required from 'typename seqan::GetValue<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::getValue(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::GetValue<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = seqan::SimpleType<unsigned char, seqan::_Dna>]'
./seqan/basic/basic_proxy.h:242:17: required from 'typename seqan::GetValue<const seqan::Proxy<TTargetSpec> >::Type seqan::getValue(const seqan::Proxy<TTargetSpec>&) [with TSpec = seqan::IteratorProxy<seqan::Iter<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, seqan::Packed<> > >; typename seqan::GetValue<const seqan::Proxy<TTargetSpec> >::Type = seqan::SimpleType<unsigned char, seqan::_Dna>]'
./seqan/basic/basic_proxy.h:272:34: required from 'typename seqan::Convert<TTarget, const seqan::Proxy<TSourceSpec> >::Type seqan::convertImpl(seqan::Convert<TTarget, T>, const seqan::Proxy<TSourceSpec>&) [with TTarget = char; T = seqan::Proxy<seqan::IteratorProxy<seqan::Iter<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, seqan::Packed<> > > >; TSpec = seqan::IteratorProxy<seqan::Iter<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, seqan::Packed<> > >; typename seqan::Convert<TTarget, const seqan::Proxy<TSourceSpec> >::Type = char]'
./seqan/basic/basic_converter.h:111:20: required from 'typename seqan::Convert<TTarget, TSource>::Type seqan::convert(const TSource&) [with TTarget = char; TSource = seqan::Proxy<seqan::IteratorProxy<seqan::Iter<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >, seqan::Packed<> > > >; typename seqan::Convert<TTarget, TSource>::Type = char]'
cracIndex.cpp:224:50: required from here
./seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<unnamed>' and 'enum seqan::BitsPerValue<unsigned int>::<unnamed>' [-Wenum-compare]
./seqan/sequence/string_packed.h:294:37: warning: comparison between types 'seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<unnamed enum>' and 'seqan::BitsPerValue<unsigned int>::<unnamed enum>' [-Wsign-compare]
In file included from ./seqan/basic.h:101,
from ./seqan/sequence.h:27,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10,
from cracIndex.cpp:67:
./seqan/basic/basic_alphabet_trait_basic.h: In instantiation of 'void seqan::_arrayCopyForward_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna5>]':
./seqan/basic/basic_alphabet_trait_basic.h:226:27: required from 'void seqan::arrayCopyForward(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna5>]'
./seqan/basic/basic_alphabet_trait_basic.h:102:18: required from 'void seqan::_arrayConstructCopy_Pointer(TValue*, TValue*, TValue*, seqan::True) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna5>]'
./seqan/basic/basic_alphabet_trait_basic.h:121:29: required from 'void seqan::arrayConstructCopy(TValue*, TValue*, TValue*) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna5>]'
./seqan/sequence/string_alloc.h:421:21: required from 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna5>; TSpec = void; _TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type = unsigned int]'
./seqan/sequence/string_base.h:1433:33: required from 'static typename seqan::Size<T>::Type seqan::_Resize_String<TExpand>::resize_(T&, typename seqan::Size<T>::Type) [with T = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >; TExpand = const seqan::Tag<seqan::TagExact_>; typename seqan::Size<T>::Type = unsigned int]'
./seqan/sequence/string_base.h:1459:52: required from 'typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::resize(seqan::String<TValue, TSpec>&, TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna5>; TSpec = seqan::Alloc<void>; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = unsigned int]'
./seqan/sequence/sequence_interface.h:1360:15: required from 'typename seqan::Size<T>::Type seqan::resize(T&, TSize) [with T = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >; TSize = unsigned int; typename seqan::Size<T>::Type = unsigned int]'
./seqan/file/file_format_fasta.h:269:8: required from 'void seqan::read(TFile&, TData&, TSize, Fasta) [with TFile = std::basic_ifstream<char>; TData = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >; TSize = unsigned int; seqan::Fasta = const seqan::Tag<seqan::TagFasta_>]'
./seqan/file/file_format_fasta.h:309:6: required from 'void seqan::read(TFile&, TData&, Fasta) [with TFile = std::basic_ifstream<char>; TData = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >; seqan::Fasta = const seqan::Tag<seqan::TagFasta_>]'
cracIndex.cpp:142:40: required from here
./seqan/basic/basic_alphabet_trait_basic.h:207:9: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'struct seqan::SimpleType<unsigned char, seqan::_Dna5>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
207 | memmove(target_begin, source_begin, (source_end - source_begin) * sizeof(TValue));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./seqan/basic.h:106,
from ./seqan/sequence.h:27,
from /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt/blockwise_sa.h:10,
from cracIndex.cpp:67:
./seqan/basic/basic_alphabet_simple.h:57:8: note: 'struct seqan::SimpleType<unsigned char, seqan::_Dna5>' declared here
57 | struct SimpleType
| ^~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SSA.o SSA.cpp
In file included from /usr/include/libGkArrays/readsReader.h:109,
from locateTags.h:60,
from locateTags.cpp:53:
/usr/include/libGkArrays/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
/usr/include/libGkArrays/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
/usr/include/libGkArrays/readsReader.h:111:1: note: in expansion of macro 'KSEQ_INIT'
111 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.cpp
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bwt -I/usr/include/libGkArrays -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GenomeInfo.o GenomeInfo.cpp
rm -f libSSA.a
ar cru libSSA.a bitarray.o bitrankw32int.o chrPosition.o HuffAlphabetRank.o Huffman_Codes.o locateOnGenome.o locateTags.o SSA.o utils.o GenomeInfo.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libSSA.a
/bin/bash ../../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lm -lpthread -lSSA -L/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/ -Wl,-z,relro -Wl,-z,now -o crac-index cracIndex.o libSSA.a -lhts -lz -lpthread -lm
libtool: link: g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac-index cracIndex.o -lSSA -L/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/ libSSA.a -lhts -lz -lpthread -lm
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA'
Making all in libReadsReader
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader'
Making all in kseq
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader/kseq'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader/kseq'
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader'
g++ -DHAVE_CONFIG_H -I. -I../../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libReadsReader_a-readsReader.o `test -f 'readsReader.cpp' || echo './'`readsReader.cpp
rm -f libReadsReader.a
ar cru libReadsReader.a libReadsReader_a-readsReader.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libReadsReader.a
make[4]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader'
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader'
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src'
g++ -DHAVE_CONFIG_H -I. -I../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Classifier.o Classifier.cpp
g++ -DHAVE_CONFIG_H -I. -I../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o classifyTags.o classifyTags.cpp
g++ -DHAVE_CONFIG_H -I. -I../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GkReadIndex.o GkReadIndex.cpp
g++ -DHAVE_CONFIG_H -I. -I../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o JellyReadIndex.o JellyReadIndex.cpp
classifyTags.cpp:421:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
421 | headerTemplate << "#Created on " <<__DATE__ << endl << "#" << endl;
| ^~~~~~~~
In file included from /usr/include/libGkArrays/bitvector.hxx:104,
from /usr/include/libGkArrays/solArray.h:106,
from /usr/include/libGkArrays/gkArrays.h:112,
from GkReadIndex.h:60,
from GkReadIndex.cpp:55:
/usr/include/libGkArrays/largebinvect.hxx:119:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
119 | LargeBinVect(const CountWordSize length = 0, const bool value = 0) throw (std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:120:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
120 | LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:121:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
121 | LargeBinVect(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:127:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
127 | inline LargeBinVect<CountWordSize> &operator=(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc);
| ^~~~~
In file included from /usr/include/libGkArrays/bitvector.hxx:104,
from /usr/include/libGkArrays/solArray.h:106,
from /usr/include/libGkArrays/gkArrays.h:112,
from GkReadIndex.h:60,
from GkReadIndex.cpp:55:
/usr/include/libGkArrays/largebinvect.hxx:155:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
155 | inline LargeBinVect<CountWordSize> operator()(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:158:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
158 | inline unsigned long int GetValue(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:161:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
161 | inline bool operator[](const CountWordSize i) const throw (std::out_of_range);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:177:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
177 | inline bool GetBit(const CountWordSize i) const throw (std::out_of_range);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:179:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
179 | inline LargeBinVect<CountWordSize> &SetBit(const CountWordSize i, const bool value) throw (std::out_of_range);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:182:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
182 | inline LargeBinVect<CountWordSize> &SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:191:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
191 | inline LargeBinVect<CountWordSize> &Resize(const CountWordSize length, const bool value = 0) throw (std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:194:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
194 | inline LargeBinVect<CountWordSize> &Append(const bool value) throw (BinVectOverflow, std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:197:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
197 | inline LargeBinVect<CountWordSize> &Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:200:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
200 | inline LargeBinVect<CountWordSize> &operator+=(const LargeBinVect<CountWordSize> &v) throw (BinVectOverflow, std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:203:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
203 | inline LargeBinVect<CountWordSize> &operator++() throw (BinVectOverflow, std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:205:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
205 | inline LargeBinVect<CountWordSize> operator++(int) throw (BinVectOverflow, std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:208:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
208 | inline LargeBinVect<CountWordSize> &operator--() throw (BinVectOverflow);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:210:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
210 | inline LargeBinVect<CountWordSize> operator--(int) throw (BinVectOverflow, std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
214 | inline LargeBinVect<CountWordSize> Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc);
| ^~~~~
In file included from /usr/include/libGkArrays/largebinvect.hxx:241,
from /usr/include/libGkArrays/bitvector.hxx:104,
from /usr/include/libGkArrays/solArray.h:106,
from /usr/include/libGkArrays/gkArrays.h:112,
from GkReadIndex.h:60,
from GkReadIndex.cpp:55:
/usr/include/libGkArrays/largebinvect.cxx:121:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
121 | unsigned char *MyCalloc(const CountWordSize w, const int value = -1) throw (std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:136:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
136 | LargeBinVect<CountWordSize>::LargeBinVect(const CountWordSize length, const bool value) throw (std::bad_alloc)
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:147:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
147 | LargeBinVect<CountWordSize>::LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:167:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
167 | LargeBinVect<CountWordSize>::LargeBinVect(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc)
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:184:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
184 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator=(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc) {
| ^~~~~
In file included from /usr/include/libGkArrays/largebinvect.hxx:241,
from /usr/include/libGkArrays/bitvector.hxx:104,
from /usr/include/libGkArrays/solArray.h:106,
from /usr/include/libGkArrays/gkArrays.h:112,
from GkReadIndex.h:60,
from GkReadIndex.cpp:55:
/usr/include/libGkArrays/largebinvect.cxx:339:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
339 | LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator()(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:363:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
363 | unsigned long int LargeBinVect<CountWordSize>::GetValue(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:397:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
397 | bool LargeBinVect<CountWordSize>::operator[](const CountWordSize i) const throw (std::out_of_range) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:478:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
478 | bool LargeBinVect<CountWordSize>::GetBit(const CountWordSize i) const throw (std::out_of_range) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:493:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
493 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::SetBit(const CountWordSize i, const bool value) throw (std::out_of_range) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:513:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
513 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:619:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
619 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::Resize(const CountWordSize length, const bool value) throw (std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:653:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
653 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::Append(const bool value) throw (BinVectOverflow, std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:661:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
661 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:673:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
673 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator+=(const LargeBinVect<CountWordSize> &v) throw (BinVectOverflow, std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:711:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
711 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator++() throw (BinVectOverflow, std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:727:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
727 | LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator++(int) throw (BinVectOverflow, std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:734:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
734 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator--() throw (BinVectOverflow) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:750:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
750 | LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator--(int) throw (BinVectOverflow, std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:757:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
757 | LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc) {
| ^~~~~
In file included from /usr/include/libGkArrays/gkArrays.h:112,
from GkReadIndex.h:60,
from GkReadIndex.cpp:55:
/usr/include/libGkArrays/solArray.h:160:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
160 | SolArray(void *ptr, array_type t, uintSA nbElements) throw (invalid_argument);
| ^~~~~
/usr/include/libGkArrays/solArray.h:202:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
202 | void realloc(uintSA nbElements) throw (logic_error);
| ^~~~~
In file included from libReadsReader/readsReader.h:57,
from Read.h:55,
from ReadIndex.h:52,
from GkReadIndex.h:59,
from GkReadIndex.cpp:55:
libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT'
59 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o crac.o crac.cpp
crac.cpp:213:34: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
213 | printf("\tCompiled on %s.\n\n",__DATE__);
| ^~~~~~~~
In file included from libReadsReader/readsReader.h:57,
from Read.h:55,
from ReadIndex.h:52,
from classifyTags.h:53,
from classifyTags.cpp:52:
libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT'
59 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
In file included from ./libReadsReader/readsReader.h:57,
from ./Read.h:55,
from ./ReadIndex.h:52,
from ./Classifier.h:56,
from Classifier.cpp:52:
./libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
./libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
./libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT'
59 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
In file included from libReadsReader/readsReader.h:57,
from Read.h:55,
from ReadIndex.h:52,
from JellyReadIndex.h:59,
from JellyReadIndex.cpp:55:
libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT'
59 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
In file included from /usr/include/libGkArrays/bitvector.hxx:104,
from /usr/include/libGkArrays/solArray.h:106,
from /usr/include/libGkArrays/gkArrays.h:112,
from crac.cpp:69:
/usr/include/libGkArrays/largebinvect.hxx:119:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
119 | LargeBinVect(const CountWordSize length = 0, const bool value = 0) throw (std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:120:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
120 | LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:121:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
121 | LargeBinVect(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:127:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
127 | inline LargeBinVect<CountWordSize> &operator=(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc);
| ^~~~~
In file included from /usr/include/libGkArrays/bitvector.hxx:104,
from /usr/include/libGkArrays/solArray.h:106,
from /usr/include/libGkArrays/gkArrays.h:112,
from crac.cpp:69:
/usr/include/libGkArrays/largebinvect.hxx:155:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
155 | inline LargeBinVect<CountWordSize> operator()(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:158:116: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
158 | inline unsigned long int GetValue(const CountWordSize b = 0, const CountWordSize lg = ~((CountWordSize)0)) const throw (std::bad_alloc, std::out_of_range);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:161:55: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
161 | inline bool operator[](const CountWordSize i) const throw (std::out_of_range);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:177:51: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
177 | inline bool GetBit(const CountWordSize i) const throw (std::out_of_range);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:179:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
179 | inline LargeBinVect<CountWordSize> &SetBit(const CountWordSize i, const bool value) throw (std::out_of_range);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:182:128: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
182 | inline LargeBinVect<CountWordSize> &SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:191:96: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
191 | inline LargeBinVect<CountWordSize> &Resize(const CountWordSize length, const bool value = 0) throw (std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:194:64: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
194 | inline LargeBinVect<CountWordSize> &Append(const bool value) throw (BinVectOverflow, std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:197:65: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
197 | inline LargeBinVect<CountWordSize> &Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:200:88: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
200 | inline LargeBinVect<CountWordSize> &operator+=(const LargeBinVect<CountWordSize> &v) throw (BinVectOverflow, std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:203:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
203 | inline LargeBinVect<CountWordSize> &operator++() throw (BinVectOverflow, std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:205:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
205 | inline LargeBinVect<CountWordSize> operator++(int) throw (BinVectOverflow, std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:208:52: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
208 | inline LargeBinVect<CountWordSize> &operator--() throw (BinVectOverflow);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:210:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
210 | inline LargeBinVect<CountWordSize> operator--(int) throw (BinVectOverflow, std::bad_alloc);
| ^~~~~
/usr/include/libGkArrays/largebinvect.hxx:214:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
214 | inline LargeBinVect<CountWordSize> Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc);
| ^~~~~
In file included from /usr/include/libGkArrays/largebinvect.hxx:241,
from /usr/include/libGkArrays/bitvector.hxx:104,
from /usr/include/libGkArrays/solArray.h:106,
from /usr/include/libGkArrays/gkArrays.h:112,
from crac.cpp:69:
/usr/include/libGkArrays/largebinvect.cxx:121:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
121 | unsigned char *MyCalloc(const CountWordSize w, const int value = -1) throw (std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:136:89: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
136 | LargeBinVect<CountWordSize>::LargeBinVect(const CountWordSize length, const bool value) throw (std::bad_alloc)
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:147:70: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
147 | LargeBinVect<CountWordSize>::LargeBinVect(const char *binary_string) throw (BinVectOverflow, std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:167:81: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
167 | LargeBinVect<CountWordSize>::LargeBinVect(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc)
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:184:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
184 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator=(const LargeBinVect<CountWordSize> &v) throw (std::bad_alloc) {
| ^~~~~
In file included from /usr/include/libGkArrays/largebinvect.hxx:241,
from /usr/include/libGkArrays/bitvector.hxx:104,
from /usr/include/libGkArrays/solArray.h:106,
from /usr/include/libGkArrays/gkArrays.h:112,
from crac.cpp:69:
/usr/include/libGkArrays/largebinvect.cxx:339:123: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
339 | LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator()(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:363:110: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
363 | unsigned long int LargeBinVect<CountWordSize>::GetValue(const CountWordSize b, const CountWordSize lg) const throw (std::bad_alloc, std::out_of_range) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:397:75: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
397 | bool LargeBinVect<CountWordSize>::operator[](const CountWordSize i) const throw (std::out_of_range) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:478:71: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
478 | bool LargeBinVect<CountWordSize>::GetBit(const CountWordSize i) const throw (std::out_of_range) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:493:107: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
493 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::SetBit(const CountWordSize i, const bool value) throw (std::out_of_range) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:513:148: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
513 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::SetBitRange(const CountWordSize i, const CountWordSize j, const long unsigned int value) throw (std::out_of_range) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:619:112: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
619 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::Resize(const CountWordSize length, const bool value) throw (std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:653:84: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
653 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::Append(const bool value) throw (BinVectOverflow, std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:661:85: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
661 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::Prepend(const bool value) throw (BinVectOverflow, std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:673:108: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
673 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator+=(const LargeBinVect<CountWordSize> &v) throw (BinVectOverflow, std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:711:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
711 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator++() throw (BinVectOverflow, std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:727:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
727 | LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator++(int) throw (BinVectOverflow, std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:734:72: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
734 | LargeBinVect<CountWordSize> &LargeBinVect<CountWordSize>::operator--() throw (BinVectOverflow) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:750:74: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
750 | LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::operator--(int) throw (BinVectOverflow, std::bad_alloc) {
| ^~~~~
/usr/include/libGkArrays/largebinvect.cxx:757:87: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
757 | LargeBinVect<CountWordSize> LargeBinVect<CountWordSize>::Split(const CountWordSize i) throw (std::out_of_range, std::bad_alloc) {
| ^~~~~
In file included from /usr/include/libGkArrays/gkArrays.h:112,
from crac.cpp:69:
/usr/include/libGkArrays/solArray.h:160:58: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
160 | SolArray(void *ptr, array_type t, uintSA nbElements) throw (invalid_argument);
| ^~~~~
/usr/include/libGkArrays/solArray.h:202:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
202 | void realloc(uintSA nbElements) throw (logic_error);
| ^~~~~
Classifier.cpp: In member function 'virtual void SingleReadClassifier::classify()':
Classifier.cpp:203:33: warning: 'bioundetermined_type' may be used uninitialized in this function [-Wmaybe-uninitialized]
203 | taginfo->addBioUndetermined(suppoBreak->getLocationStartBreak(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
204 | suppoBreak->getPositionStartBreak(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
205 | bioundetermined_type,
| ~~~~~~~~~~~~~~~~~~~~~
206 | message.c_str());
| ~~~~~~~~~~~~~~~~
crac.cpp: In function 'int main(int, char**)':
crac.cpp:1009:26: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=]
1009 | } catch (bad_alloc e) {
| ^
In file included from libReadsReader/readsReader.h:57,
from Read.h:55,
from ReadIndex.h:52,
from classifyTags.h:53,
from crac.cpp:66:
libReadsReader/readsReader.h: At global scope:
libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT'
59 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Parameters.o Parameters.cpp
g++ -DHAVE_CONFIG_H -I. -I../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SupportBreak.o SupportBreak.cpp
g++ -DHAVE_CONFIG_H -I. -I../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o BreakList.o BreakList.cpp
g++ -DHAVE_CONFIG_H -I. -I../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o CandidatBreak.o CandidatBreak.cpp
In file included from libReadsReader/readsReader.h:57,
from Read.h:55,
from ReadIndex.h:52,
from Support.h:59,
from SupportBreak.cpp:55:
libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT'
59 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Support.o Support.cpp
g++ -DHAVE_CONFIG_H -I. -I../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o locateServer.o locateServer.cpp
In file included from libReadsReader/readsReader.h:57,
from Read.h:55,
from ReadIndex.h:52,
from Support.h:59,
from Support.cpp:57:
libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT'
59 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
locateServer.cpp: In function 'void* launchSubServer(void*)':
locateServer.cpp:464:8: warning: unused variable 'threshold' [-Wunused-variable]
464 | uint threshold = indexTags->getFactorLength();
| ^~~~~~~~~
locateServer.cpp:466:9: warning: variable 'dontCare' set but not used [-Wunused-but-set-variable]
466 | char *dontCare, *variable, *tag_length, *factor;
| ^~~~~~~~
locateServer.cpp: In function 'void locateServer(ClassifyTags*, const char*, const char*)':
locateServer.cpp:717:9: warning: variable 'dontCare' set but not used [-Wunused-but-set-variable]
717 | char *dontCare;
| ^~~~~~~~
In file included from libReadsReader/readsReader.h:57,
from Read.h:55,
from ReadIndex.h:52,
from classifyTags.h:53,
from locateServer.cpp:59:
libReadsReader/readsReader.h: At global scope:
libReadsReader/kseq/kseq.h:169:14: warning: 'int kseq_read(kseq_t*)' defined but not used [-Wunused-function]
169 | static int kseq_read(kseq_t *seq) \
| ^~~~~~~~~
libReadsReader/kseq/kseq.h:227:3: note: in expansion of macro '__KSEQ_READ'
227 | __KSEQ_READ
| ^~~~~~~~~~~
libReadsReader/readsReader.h:59:1: note: in expansion of macro 'KSEQ_INIT'
59 | KSEQ_INIT(gzFile, gzread)
| ^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o utils.cpp
g++ -DHAVE_CONFIG_H -I. -I../config -I/<<BUILDDIR>>/crac-2.5.2+dfsg -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -I/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/karkkainen_bw -I/usr/include/jellyfish -I/usr/include/libGkArrays -I/usr/include/libProgressBar -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -ansi -funroll-loops -O4 -DNDEBUG -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Bitset.o Bitset.cpp
ln -s -f /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/crac-index crac-index
/bin/bash ../libtool --tag=CXX --mode=link g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -lGkArrays -ljellyfish-2.0 -lm -lpthread -lhts -lSSA -lReadsInfo -lReadsReader -lgzstream -L/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -L/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsInfo -L/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader -ljellyfish-2.0 -lGkArrays -lProgressBar -Wl,-z,relro -Wl,-z,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/libSSA.a /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm
libtool: link: g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/crac-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o crac Classifier.o classifyTags.o GkReadIndex.o JellyReadIndex.o crac.o Parameters.o SupportBreak.o BreakList.o CandidatBreak.o Support.o locateServer.o utils.o Bitset.o -lSSA -lReadsInfo -lReadsReader -lgzstream -L/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA -L/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsInfo -L/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader /usr/lib/arm-linux-gnueabihf/libjellyfish-2.0.so -lGkArrays -lProgressBar /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA/libSSA.a /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsInfo/libReadsInfo.a /<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader/libReadsReader.a -lhts -lz -lpthread -lm
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src'
Making all in man
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make[2]: Nothing to be done for 'all'.
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make[2]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/scripts'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/scripts'
Making all in test_f
make[2]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f'
Making all in causes
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/causes'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/causes'
Making all in bug
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/bug'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/bug'
Making all in cigar
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/cigar'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/cigar'
Making all in splices_adjust
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/splices_adjust'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/splices_adjust'
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f'
make[3]: Nothing to be done for 'all-am'.
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make[2]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f'
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make[2]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
# Sequence of tests is important so parallel execution is no option
dh_auto_test --no-parallel
make -j1 check VERBOSE=1
make[2]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
Making check in src
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src'
Making check in libReadsInfo
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsInfo'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsInfo'
Making check in libSSA
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA'
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Making check in libReadsReader
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader'
Making check in kseq
make[5]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader/kseq'
make[5]: Nothing to be done for 'check'.
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make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/man'
make[3]: Nothing to be done for 'check'.
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Making check in scripts
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make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/scripts'
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make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f'
Making check in causes
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/causes'
make[4]: Nothing to be done for 'check'.
make[4]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/causes'
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make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/bug'
make[4]: Nothing to be done for 'check'.
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Making check in cigar
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/cigar'
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Making check in splices_adjust
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/splices_adjust'
make[4]: Nothing to be done for 'check'.
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make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f'
make check-TESTS
make[5]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f'
make[6]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f'
PASS: index_genomes.sh
PASS: launch_sg.sh
PASS: test_index.sh
============================================================================
Testsuite summary for crac 2.5.2
============================================================================
# TOTAL: 3
# PASS: 3
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[6]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f'
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make[2]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j1 install DESTDIR=/<<BUILDDIR>>/crac-2.5.2\+dfsg/debian/crac AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
Making install in src
make[2]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src'
Making install in libReadsInfo
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsInfo'
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsInfo'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsInfo'
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsInfo'
Making install in libSSA
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA'
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA'
/bin/mkdir -p '/<<BUILDDIR>>/crac-2.5.2+dfsg/debian/crac/usr/bin'
/bin/bash ../../libtool --mode=install /usr/bin/install -c crac-index '/<<BUILDDIR>>/crac-2.5.2+dfsg/debian/crac/usr/bin'
libtool: install: /usr/bin/install -c crac-index /<<BUILDDIR>>/crac-2.5.2+dfsg/debian/crac/usr/bin/crac-index
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA'
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libSSA'
Making install in libReadsReader
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader'
Making install in kseq
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader/kseq'
make[5]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader/kseq'
make[5]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<BUILDDIR>>/crac-2.5.2+dfsg/debian/crac/usr/include/crac-2.5.2/kseq'
/usr/bin/install -c -m 644 kseq.h '/<<BUILDDIR>>/crac-2.5.2+dfsg/debian/crac/usr/include/crac-2.5.2/kseq'
make[5]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader/kseq'
make[4]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader/kseq'
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader'
make[5]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader'
make[5]: Nothing to be done for 'install-exec-am'.
make[5]: Nothing to be done for 'install-data-am'.
make[5]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader'
make[4]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader'
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src/libReadsReader'
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src'
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src'
/bin/mkdir -p '/<<BUILDDIR>>/crac-2.5.2+dfsg/debian/crac/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c crac '/<<BUILDDIR>>/crac-2.5.2+dfsg/debian/crac/usr/bin'
libtool: install: /usr/bin/install -c crac /<<BUILDDIR>>/crac-2.5.2+dfsg/debian/crac/usr/bin/crac
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src'
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/src'
Making install in man
make[2]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/man'
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/man'
make[3]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/<<BUILDDIR>>/crac-2.5.2+dfsg/debian/crac/usr/share/man/man1'
/usr/bin/install -c -m 644 crac.1 '/<<BUILDDIR>>/crac-2.5.2+dfsg/debian/crac/usr/share/man/man1'
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/man'
make[2]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/man'
Making install in scripts
make[2]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/scripts'
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/scripts'
/bin/mkdir -p '/<<BUILDDIR>>/crac-2.5.2+dfsg/debian/crac/usr/bin'
/usr/bin/install -c crac-client '/<<BUILDDIR>>/crac-2.5.2+dfsg/debian/crac/usr/bin'
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/scripts'
make[2]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/scripts'
Making install in test_f
make[2]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f'
Making install in causes
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/causes'
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/causes'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/causes'
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/causes'
Making install in bug
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/bug'
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/bug'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/bug'
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/bug'
Making install in cigar
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/cigar'
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/cigar'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/cigar'
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/cigar'
Making install in splices_adjust
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/splices_adjust'
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/splices_adjust'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/splices_adjust'
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f/splices_adjust'
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f'
make[4]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f'
make[4]: Nothing to be done for 'install-exec-am'.
make[4]: Nothing to be done for 'install-data-am'.
make[4]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f'
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f'
make[2]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg/test_f'
make[2]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installexamples
make[1]: Entering directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
mkdir debian/crac/usr/share/doc/crac/examples
rsync -a --exclude=Makefile* test_f debian/crac/usr/share/doc/crac/examples
sed -i 's+${abs_top_builddir:-\.\./\.\.}/src/crac+crac+' `grep -wRl crac debian/crac/usr/share/doc/crac/examples/*`
sed -i 's+$abs_top_builddir/src/crac-index+crac-index+' `grep -wRl crac-index debian/crac/usr/share/doc/crac/examples/*`
make[1]: Leaving directory '/<<BUILDDIR>>/crac-2.5.2+dfsg'
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/crac/usr/bin/crac-index contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/crac/usr/bin/crac contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/crac/usr/bin/crac-index debian/crac/usr/bin/crac were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'crac-dbgsym' in '../crac-dbgsym_2.5.2+dfsg-2_armhf.deb'.
dpkg-deb: building package 'crac' in '../crac_2.5.2+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../crac_2.5.2+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-12-14T13:47:22Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
crac_2.5.2+dfsg-2_armhf.changes:
--------------------------------
Format: 1.8
Date: Fri, 26 Jul 2019 22:40:52 +0200
Source: crac
Binary: crac crac-dbgsym
Architecture: armhf
Version: 2.5.2+dfsg-2
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
crac - integrated RNA-Seq read analysis
Closes: 933024
Changes:
crac (2.5.2+dfsg-2) unstable; urgency=medium
.
[ Helmut Grohne ]
* Do not use pkg-config in Makefile.am to enable cross building
Closes: #933024
.
[ Andreas Tille ]
* debhelper-compat 12
Checksums-Sha1:
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9e68a49e6c33a613d19b89db91682d5e05c45d05 5875 crac_2.5.2+dfsg-2_armhf.buildinfo
d5c797ef16412c3ae68082faff6191bf20fe42b6 873536 crac_2.5.2+dfsg-2_armhf.deb
Checksums-Sha256:
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5752162ca73c727d2d09da7f51664e9e52c85dec51b129ca6f10ca6d4ad2490e 5875 crac_2.5.2+dfsg-2_armhf.buildinfo
acd72fafb0dff6f24252e95e241632a147a896a02ee4eaa640bfee8774d5fb1f 873536 crac_2.5.2+dfsg-2_armhf.deb
Files:
d6026859eaef33345972d2e00655a09d 1724440 debug optional crac-dbgsym_2.5.2+dfsg-2_armhf.deb
3aa89fa81bb2d831f680c048b51c1017 5875 science optional crac_2.5.2+dfsg-2_armhf.buildinfo
1635691f83ca1a373eb425c0c1ad70a5 873536 science optional crac_2.5.2+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
crac-dbgsym_2.5.2+dfsg-2_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 1724440 bytes: control archive=644 bytes.
410 bytes, 12 lines control
296 bytes, 3 lines md5sums
Package: crac-dbgsym
Source: crac
Version: 2.5.2+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1815
Depends: crac (= 2.5.2+dfsg-2)
Section: debug
Priority: optional
Description: debug symbols for crac
Build-Ids: 6794a0b70e9e772c15d23061e9875a50aae14271 a0909f309dc81c19dd55ce4da1eff720c8baf93c
drwxr-xr-x root/root 0 2019-07-26 20:40 ./
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/lib/
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/lib/debug/.build-id/67/
-rw-r--r-- root/root 1309376 2019-07-26 20:40 ./usr/lib/debug/.build-id/67/94a0b70e9e772c15d23061e9875a50aae14271.debug
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/lib/debug/.build-id/a0/
-rw-r--r-- root/root 497032 2019-07-26 20:40 ./usr/lib/debug/.build-id/a0/909f309dc81c19dd55ce4da1eff720c8baf93c.debug
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 37392 2019-07-26 20:40 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/crac.debug
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/share/
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-07-26 20:40 ./usr/share/doc/crac-dbgsym -> crac
crac_2.5.2+dfsg-2_armhf.deb
---------------------------
new Debian package, version 2.0.
size 873536 bytes: control archive=6560 bytes.
1495 bytes, 25 lines control
22417 bytes, 249 lines md5sums
Package: crac
Version: 2.5.2+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3532
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgkarrays1 (>= 2.1.0+dfsg), libgzstream0 (>= 1.5+dfsg), libhts3 (>= 1.10), libjellyfish-2.0-2 (>= 2.3.0), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: http://crac.gforge.inria.fr/
Description: integrated RNA-Seq read analysis
CRAC is a tool to analyze High Throughput Sequencing (HTS) data in
comparison to a reference genome. It is intended for transcriptomic
and genomic sequencing reads. More precisely, with transcriptomic
reads as input, it predicts point mutations, indels, splice junction,
and chimeric RNAs (ie, non colinear splice junctions). CRAC can also
output positions and nature of sequence error that it detects in the
reads. CRAC uses a genome index. This index must be computed before
running the read analysis. For this sake, use the command "crac-index"
on your genome files. You can then process the reads using the command
crac. See the man page of CRAC (help file) by typing "man crac". CRAC
requires large amount of main memory on your computer. For processing
against the Human genome, say 50 million reads of 100 nucleotide each,
CRAC requires about 40 gigabytes of main memory. Check whether the
system of your computing server is equipped with sufficient amount of
memory before launching an analysis.
drwxr-xr-x root/root 0 2019-07-26 20:40 ./
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/bin/
-rwxr-xr-x root/root 355216 2019-07-26 20:40 ./usr/bin/crac
-rwxr-xr-x root/root 11120 2019-07-26 20:40 ./usr/bin/crac-client
-rwxr-xr-x root/root 139524 2019-07-26 20:40 ./usr/bin/crac-index
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/include/
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/include/crac-2.5.2/
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/include/crac-2.5.2/kseq/
-rw-r--r-- root/root 12765 2019-07-26 20:40 ./usr/include/crac-2.5.2/kseq/kseq.h
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/share/
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/share/doc/crac/
-rw-r--r-- root/root 2004 2015-07-13 14:37 ./usr/share/doc/crac/README.gz
-rw-r--r-- root/root 278 2019-07-26 20:40 ./usr/share/doc/crac/README.test
-rw-r--r-- root/root 679 2019-07-26 20:40 ./usr/share/doc/crac/changelog.Debian.gz
-rw-r--r-- root/root 662 2016-04-27 12:58 ./usr/share/doc/crac/changelog.gz
-rw-r--r-- root/root 25987 2019-07-26 20:40 ./usr/share/doc/crac/copyright
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/share/doc/crac/examples/
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/
-rw-r--r-- root/root 32 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15605-genome.conf
-rw-r--r-- root/root 220 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15605-genome.fa
-rw-r--r-- root/root 4319 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15605-genome.ssa
-rw-r--r-- root/root 195 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15605-read.fa
-rw-r--r-- root/root 2645 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15605.sam
-rw-r--r-- root/root 380 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15605.should_get
-rw-r--r-- root/root 54 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15605.tap
-rw-r--r-- root/root 91 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15605_2-genome.conf
-rw-r--r-- root/root 628 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15605_2-genome.fa
-rw-r--r-- root/root 4419 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15605_2-genome.ssa
-rw-r--r-- root/root 200 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15605_2-read.fa
-rw-r--r-- root/root 2789 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15605_2.sam
-rw-r--r-- root/root 401 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15605_2.should_get
-rw-r--r-- root/root 65 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15605_2.tap
-rw-r--r-- root/root 91 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15630-genome.conf
-rw-r--r-- root/root 991 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15630-genome.fa
-rw-r--r-- root/root 4643 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15630-genome.ssa
-rw-r--r-- root/root 25 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15630-read.fa
-rw-r--r-- root/root 548 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15630.sam
-rw-r--r-- root/root 427 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15630.should_get
-rw-r--r-- root/root 124 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15630.tap
-rw-r--r-- root/root 26 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15639-genome.conf
-rw-r--r-- root/root 10173 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15639-genome.fa
-rw-r--r-- root/root 10379 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15639-genome.ssa
-rw-r--r-- root/root 107 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15639-read.fa
-rw-r--r-- root/root 569 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15639.sam
-rw-r--r-- root/root 485 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15639.should_get
-rw-r--r-- root/root 137 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15639.tap
-rw-r--r-- root/root 1099 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15646-genome.conf
-rw-r--r-- root/root 2343 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15646-genome.fa
-rw-r--r-- root/root 4995 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15646-genome.ssa
-rw-r--r-- root/root 350 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15646-read.fa
-rw-r--r-- root/root 5073 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15646.sam
-rw-r--r-- root/root 591 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15646.should_get
-rw-r--r-- root/root 74 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15646.tap
-rw-r--r-- root/root 401 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15649-2.sam
-rw-r--r-- root/root 432 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15649-2.should_get
-rw-r--r-- root/root 93 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15649-2.tap
-rw-r--r-- root/root 6 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15649-genome-2.conf
-rw-r--r-- root/root 27 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15649-genome-2.fa
-rw-r--r-- root/root 4202 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15649-genome-2.ssa
-rw-r--r-- root/root 14 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15649-genome.conf
-rw-r--r-- root/root 57 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15649-genome.fa
-rw-r--r-- root/root 4210 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15649-genome.ssa
-rw-r--r-- root/root 30 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15649-read.fa
-rw-r--r-- root/root 415 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15649.sam
-rw-r--r-- root/root 391 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15649.should_get
-rw-r--r-- root/root 57 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15649.tap
-rw-r--r-- root/root 431 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15672-genome.conf
-rw-r--r-- root/root 2209 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15672-genome.fa
-rw-r--r-- root/root 5327 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15672-genome.ssa
-rw-r--r-- root/root 315 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15672-read.fa
-rw-r--r-- root/root 3964 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15672.sam
-rw-r--r-- root/root 405 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15672.should_get
-rw-r--r-- root/root 110 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15672.tap
-rw-r--r-- root/root 18 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15677-genome.conf
-rw-r--r-- root/root 241 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15677-genome.fa
-rw-r--r-- root/root 4335 2019-07-26 20:40 ./usr/share/doc/crac/examples/test_f/bug/bug-15677-genome.ssa
-rw-r--r-- root/root 109 2014-10-20 21:35 ./usr/share/doc/crac/examples/test_f/bug/bug-15677-read.fa
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-rw-r--r-- root/root 366 2019-07-26 20:40 ./usr/share/doc/crac/run-unit-test
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/share/man/
drwxr-xr-x root/root 0 2019-07-26 20:40 ./usr/share/man/man1/
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 42000
Build-Time: 389
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 255
Job: crac_2.5.2+dfsg-2
Machine Architecture: armhf
Package: crac
Package-Time: 694
Source-Version: 2.5.2+dfsg-2
Space: 42000
Status: successful
Version: 2.5.2+dfsg-2
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Finished at 2020-12-14T13:47:22Z
Build needed 00:11:34, 42000k disc space