smalt →
0.7.6-8 →
armhf → 2018-10-27 05:25:35
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| smalt 0.7.6-8 (armhf) Sat, 27 Oct 2018 04:46:51 +0000 |
+==============================================================================+
Package: smalt
Version: 0.7.6-8
Source Version: 0.7.6-8
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-d635fe95-e0f9-44e6-9b8e-bbb5f8455733' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.9 MB]
Fetched 24.0 MB in 27s (903 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: 'smalt' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/smalt.git
Please use:
git clone https://salsa.debian.org/med-team/smalt.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 72.3 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main smalt 0.7.6-8 (dsc) [2050 B]
Get:2 http://172.17.0.1/private buster-staging/main smalt 0.7.6-8 (tar) [72.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main smalt 0.7.6-8 (diff) [5036 B]
Fetched 72.3 MB in 7s (9814 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/smalt-OBMzX3/smalt-0.7.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/smalt-OBMzX3' 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-hkyxbf/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-hkyxbf/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-hkyxbf/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-hkyxbf/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hkyxbf/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hkyxbf/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-hkyxbf/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hkyxbf/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2945 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:
ca-certificates dbus dbus-user-session krb5-locales libexpat1 libnss-systemd
libpam-systemd libssl1.1 openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 42 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-hkyxbf/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14019 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 all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), zlib1g-dev, python, samtools, libbambamc-dev
Filtered Build-Depends: debhelper (>= 11~), zlib1g-dev, python, samtools, libbambamc-dev
dpkg-deb: building package 'sbuild-build-depends-smalt-dummy' in '/<<BUILDDIR>>/resolver-hkyxbf/apt_archive/sbuild-build-depends-smalt-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-smalt-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-hkyxbf/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hkyxbf/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hkyxbf/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-hkyxbf/apt_archive ./ Sources [515 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hkyxbf/apt_archive ./ Packages [600 B]
Fetched 2448 B in 1s (3561 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install smalt build dependencies (apt-based resolver)
-----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session krb5-locales libnss-systemd
libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbambamc-dev libbambamc0
libbsd0 libcroco3 libcurl3-gnutls libelf1 libfile-stripnondeterminism-perl
libfreetype6 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts2 libicu-le-hb0
libicu60 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib
librtmp1 libsigsegv2 libssh2-1 libtool libxml2 m4 man-db mime-support
pkg-config po-debconf python python-minimal python2 python2-minimal
python2.7 python2.7-minimal samtools zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl python-doc python-tk python2-doc python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs publicsuffix libltdl-dev libmail-sendmail-perl cwltool
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbambamc-dev libbambamc0
libbsd0 libcroco3 libcurl3-gnutls libelf1 libfile-stripnondeterminism-perl
libfreetype6 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts2 libicu-le-hb0
libicu60 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib
librtmp1 libsigsegv2 libssh2-1 libtool libxml2 m4 man-db mime-support
pkg-config po-debconf python python-minimal python2 python2-minimal
python2.7 python2.7-minimal samtools sbuild-build-depends-smalt-dummy
zlib1g-dev
0 upgraded, 57 newly installed, 0 to remove and 42 not upgraded.
Need to get 24.0 MB/24.6 MB of archives.
After this operation, 86.3 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hkyxbf/apt_archive ./ sbuild-build-depends-smalt-dummy 0.invalid.0 [880 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-2+b1 [1160 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-4 [394 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-4 [1088 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-3 [41.3 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-3 [20.9 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-4 [1843 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-4 [299 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-3 [20.7 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-3 [20.7 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-3 [41.5 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-3 [22.7 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-8 [117 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-2 [771 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-8 [434 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.043-2 [20.2 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.043-2 [12.2 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.9.0-1+rpi1 [877 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-8 [1220 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.4.1 [989 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libbambamc0 armhf 0.0.50-3 [30.4 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libbambamc-dev armhf 0.0.50-3 [42.6 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.34.0-1 [73.4 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.61.0-1 [281 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.7-2 [259 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf samtools armhf 1.7-2 [365 kB]
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Unpacking libicu60:armhf (60.2-6) ...
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Unpacking gettext (0.19.8.1-8) ...
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Unpacking intltool-debian (0.35.0+20060710.4) ...
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Unpacking po-debconf (1.0.20) ...
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Unpacking debhelper (11.4.1) ...
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Unpacking libbambamc0 (0.0.50-3) ...
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Unpacking pkg-config (0.29-4) ...
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Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
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Unpacking libbambamc-dev (0.0.50-3) ...
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Unpacking libnghttp2-14:armhf (1.34.0-1) ...
Selecting previously unselected package libpsl5:armhf.
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Unpacking libpsl5:armhf (0.20.2-2) ...
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Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
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Unpacking sbuild-build-depends-smalt-dummy (0.invalid.0) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libnghttp2-14:armhf (1.34.0-1) ...
Setting up mime-support (3.61) ...
Installing new version of config file /etc/mime.types ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libpsl5:armhf (0.20.2-2) ...
Setting up libelf1:armhf (0.170-0.5) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.58.1-2) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-8) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Setting up m4 (1.4.18-1) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libfreetype6:armhf (2.8.1-2) ...
Setting up libmagic-mgc (1:5.34-2) ...
Setting up libmagic1:armhf (1:5.34-2) ...
Setting up libgraphite2-3:armhf (1.3.12-1) ...
Setting up pkg-config (0.29-4) ...
Setting up libssh2-1:armhf (1.8.0-2) ...
Processing triggers for libc-bin (2.27-6+rpi1) ...
Setting up dwz (0.12-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up libbambamc0 (0.0.50-3) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libpython2.7-stdlib:armhf (2.7.15-4) ...
Setting up autopoint (0.19.8.1-8) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (0.043-2) ...
Setting up libcurl3-gnutls:armhf (7.61.0-1) ...
Setting up python2.7 (2.7.15-4) ...
Setting up libharfbuzz0b:armhf (1.9.0-1+rpi1) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.34-2) ...
Setting up libbambamc-dev (0.0.50-3) ...
Setting up automake (1:1.16.1-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.4-2+b1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpython2-stdlib:armhf (2.7.15-3) ...
Setting up libhts2:armhf (1.7-2) ...
Setting up libtool (2.4.6-6) ...
Setting up python2 (2.7.15-3) ...
Setting up libpython-stdlib:armhf (2.7.15-3) ...
Setting up samtools (1.7-2) ...
Setting up python (2.7.15-3) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up gettext (0.19.8.1-8) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.20) ...
Setting up debhelper (11.4.1) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (0.043-2) ...
Setting up sbuild-build-depends-smalt-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-6+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-6+rpi1 dpkg-dev_1.19.0.5 g++-8_8.2.0-7+rpi1 gcc-8_8.2.0-7+rpi1 libc6-dev_2.27-6+rpi1 libstdc++-8-dev_8.2.0-7+rpi1 libstdc++6_8.2.0-7+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.118 apt_1.7.0 autoconf_2.69-11 automake_1:1.16.1-2 autopoint_0.19.8.1-8 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-6+rpi1 binutils-arm-linux-gnueabihf_2.31.1-6+rpi1 binutils-common_2.31.1-6+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.2.0-7+rpi1 dash_0.5.10.2-1 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.4.1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.043-2 diffutils_1:3.6-1 dirmngr_2.2.10-3+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20180808-2 g++_4:8.1.0-1+rpi1 g++-8_8.2.0-7+rpi1 gcc_4:8.1.0-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.4.0-22+rpi1 gcc-8_8.2.0-7+rpi1 gcc-8-base_8.2.0-7+rpi1 gettext_0.19.8.1-8 gettext-base_0.19.8.1-8 gnupg_2.2.10-3+rpi1 gnupg-l10n_2.2.10-3+rpi1 gnupg-utils_2.2.10-3+rpi1 gpg_2.2.10-3+rpi1 gpg-agent_2.2.10-3+rpi1 gpg-wks-client_2.2.10-3+rpi1 gpg-wks-server_2.2.10-3+rpi1 gpgconf_2.2.10-3+rpi1 gpgsm_2.2.10-3+rpi1 gpgv_2.2.10-3+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2.1 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.54 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 krb5-locales_1.16.1-1 libacl1_2.2.52-3 libapparmor1_2.13-8 libapt-pkg5.0_1.7.0 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-7+rpi1 libassuan0_2.5.1-2 libatomic1_8.2.0-7+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbambamc-dev_0.0.50-3 libbambamc0_0.0.50-3 libbinutils_2.31.1-6+rpi1 libblkid1_2.32.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.27-6+rpi1 libc-dev-bin_2.27-6+rpi1 libc6_2.27-6+rpi1 libc6-dev_2.27-6+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-7+rpi1 libcom-err2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.61.0-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.10-1 libdebconfclient0_0.245 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.94-1+rpi1 libdrm2_2.4.94-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.6-1 libext2fs2_1.44.4-2 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.043-2 libfreetype6_2.8.1-2 libgcc-8-dev_8.2.0-7+rpi1 libgcc1_1:8.2.0-7+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.18-2 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgdbm6_1.18-2 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.2.0-7+rpi1 libgpg-error0_1.32-1 libgraphite2-3_1.3.12-1 libgssapi-krb5-2_1.16.1-1 libharfbuzz0b_1.9.0-1+rpi1 libhogweed4_3.4-1 libhts2_1.7-2 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.6.2-1.1 libisl19_0.20-2 libjson-c3_0.12.1-1.3 libk5crypto3_1.16.1-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-1 libkrb5-3_1.16.1-1 libkrb5support0_1.16.1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnghttp2-14_1.34.0-1 libnpth0_1.6-1 libnss-systemd_239-10+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_239-10+rpi1 libpam0g_1.1.8-3.8 libpcre3_2:8.39-11+rpi1 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpython-stdlib_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7-minimal_2.7.15-4 libpython2.7-stdlib_2.7.15-4 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.25.2-1 libss2_1.44.4-2 libssh2-1_1.8.0-2 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.2.0-7+rpi1 libstdc++6_8.2.0-7+rpi1 libsystemd0_239-10+rpi1 libtasn1-6_4.13-3 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20180714-1 libtool_2.4.6-6 libubsan1_8.2.0-7+rpi1 libudev1_239-10+rpi1 libunistring2_0.9.10-1 libuuid1_2.32.1-0.1 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.5+dfsg-1+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.4-2+b1 mawk_1.3.3-17 mime-support_3.61 mount_2.32.1-0.1 multiarch-support_2.27-6+rpi1 nano_3.1-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.26_5.26.2-7 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 python_2.7.15-3 python-minimal_2.7.15-3 python2_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-4 python2.7-minimal_2.7.15-4 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 samtools_1.7-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-smalt-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_239-10+rpi1 systemd-sysv_239-10+rpi1 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_239-10+rpi1 util-linux_2.32.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Oct 24 19:15:51 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./smalt_0.7.6-8.dsc
dpkg-source: info: extracting smalt in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking smalt_0.7.6.orig.tar.gz
dpkg-source: info: unpacking smalt_0.7.6-8.debian.tar.xz
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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-d635fe95-e0f9-44e6-9b8e-bbb5f8455733
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package smalt
dpkg-buildpackage: info: source version 0.7.6-8
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build smalt-0.7.6
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
rm -rf test/*.pyc misc/*.pyc test/tmp
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
debian/rules override_dh_autoreconf
make[1]: Entering directory '/<<PKGBUILDDIR>>'
echo "Do nothing - fails because auf broken upstream autoconf stuff"
Do nothing - fails because auf broken upstream autoconf stuff
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# see upstream INSTALL file
CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
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 for icc... no
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 for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ranlib... ranlib
checking for a Python interpreter with version >= 2.6... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.7/dist-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/dist-packages
checking for samtools... yes
checking for sam_open in -lbam... no
checking for BAMBAMC... yes
checking for gzread in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking semaphore.h usability... yes
checking semaphore.h presence... yes
checking for semaphore.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdint.h... (cached) yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking emmintrin.h usability... no
checking emmintrin.h presence... no
checking for emmintrin.h... no
checking build system type... armv7l-unknown-linux-gnueabihf
checking host system type... armv7l-unknown-linux-gnueabihf
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating test/Makefile
config.status: creating test/data/Makefile
config.status: creating misc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT elib.o -MD -MP -MF .deps/elib.Tpo -c -o elib.o elib.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT filio.o -MD -MP -MF .deps/filio.Tpo -c -o filio.o filio.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT sequence.o -MD -MP -MF .deps/sequence.Tpo -c -o sequence.o sequence.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-score.o -MD -MP -MF .deps/libsgm_a-score.Tpo -c -o libsgm_a-score.o `test -f 'score.c' || echo './'`score.c
score.c:49:21: warning: 'LN0P25' defined but not used [-Wunused-const-variable=]
static const double LN0P25 = -1.386294; /* natural logarithm of 1/4 */
^~~~~~
sequence.c: In function 'seqFastqGetConstSequence':
sequence.c:2079:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (length)
^~
sequence.c:2081:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
return NULL;
^~~~~~
sequence.c: In function 'seqFastqGetSequence':
sequence.c:2094:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (length)
^~
sequence.c:2096:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
return NULL;
^~~~~~
sequence.c: In function 'seqIOopen':
sequence.c:489:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
strcpy(p->fmode, "r");
^~~~~~~~~~~~~~~~~~~~~
sequence.c:491:3: note: here
case SEQIO_WRITE_GZIP_FASTA:
^~~~
mv -f .deps/filio.Tpo .deps/filio.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-diffstr.o -MD -MP -MF .deps/libsgm_a-diffstr.Tpo -c -o libsgm_a-diffstr.o `test -f 'diffstr.c' || echo './'`diffstr.c
mv -f .deps/libsgm_a-score.Tpo .deps/libsgm_a-score.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-alibuffer.o -MD -MP -MF .deps/libsgm_a-alibuffer.Tpo -c -o libsgm_a-alibuffer.o `test -f 'alibuffer.c' || echo './'`alibuffer.c
mv -f .deps/elib.Tpo .deps/elib.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-alignment.o -MD -MP -MF .deps/libsgm_a-alignment.Tpo -c -o libsgm_a-alignment.o `test -f 'alignment.c' || echo './'`alignment.c
mv -f .deps/libsgm_a-alibuffer.Tpo .deps/libsgm_a-alibuffer.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-sort.o -MD -MP -MF .deps/libsgm_a-sort.Tpo -c -o libsgm_a-sort.o `test -f 'sort.c' || echo './'`sort.c
alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function]
static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp)
^~~~~~~~~~~~~
mv -f .deps/libsgm_a-sort.Tpo .deps/libsgm_a-sort.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-array.o -MD -MP -MF .deps/libsgm_a-array.Tpo -c -o libsgm_a-array.o `test -f 'array.c' || echo './'`array.c
mv -f .deps/libsgm_a-array.Tpo .deps/libsgm_a-array.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-interval.o -MD -MP -MF .deps/libsgm_a-interval.Tpo -c -o libsgm_a-interval.o `test -f 'interval.c' || echo './'`interval.c
mv -f .deps/libsgm_a-alignment.Tpo .deps/libsgm_a-alignment.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-hashidx.o -MD -MP -MF .deps/libsgm_a-hashidx.Tpo -c -o libsgm_a-hashidx.o `test -f 'hashidx.c' || echo './'`hashidx.c
mv -f .deps/libsgm_a-interval.Tpo .deps/libsgm_a-interval.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-hashhit.o -MD -MP -MF .deps/libsgm_a-hashhit.Tpo -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c
mv -f .deps/libsgm_a-diffstr.Tpo .deps/libsgm_a-diffstr.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-segment.o -MD -MP -MF .deps/libsgm_a-segment.Tpo -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c
hashidx.c: In function 'countPerfectKey':
hashidx.c:191:77: warning: unused parameter 'tuplectr' [-Wunused-parameter]
static int countPerfectKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
~~~~~~~~~~^~~~~~~~
hashidx.c: In function 'countCollisionKey':
hashidx.c:206:79: warning: unused parameter 'tuplectr' [-Wunused-parameter]
static int countCollisionKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
~~~~~~~~~~^~~~~~~~
hashidx.c: In function 'collectWords':
hashidx.c:223:74: warning: unused parameter 'tuplectr' [-Wunused-parameter]
static int collectWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
~~~~~~~~~~^~~~~~~~
hashidx.c: In function 'countWords':
hashidx.c:265:72: warning: unused parameter 'tuplectr' [-Wunused-parameter]
static int countWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
~~~~~~~~~~^~~~~~~~
At top level:
hashidx.c:446:18: warning: 'getWordHisto' defined but not used [-Wunused-function]
static WORDNUM_t getWordHisto(WORDNUM_t *counts, HASHNUM_t n, const HashTable *htp)
^~~~~~~~~~~~
hashidx.c:63:19: warning: 'HASHTABFIL_READERRMSG' defined but not used [-Wunused-const-variable=]
static const char HASHTABFIL_READERRMSG[] = "when reading hash table file";
^~~~~~~~~~~~~~~~~~~~~
segment.c:1375:12: warning: 'checkCANDARRsequential' defined but not used [-Wunused-function]
static int checkCANDARRsequential(const CANDARR candr, SEGNUM_t *rvc_offs)
^~~~~~~~~~~~~~~~~~~~~~
segment.c:1330:13: warning: 'labelSEGCANDWithinInsertRange' defined but not used [-Wunused-function]
static void labelSEGCANDWithinInsertRange (SEGCAND *candAp, SEGNUM_t nsegA,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mv -f .deps/sequence.Tpo .deps/sequence.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-smalt.o -MD -MP -MF .deps/smalt-smalt.Tpo -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.c
smalt.c: In function 'cleanupSmaltOutput':
smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter]
static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op)
~~~~~~~~^~~~~~~
mv -f .deps/libsgm_a-hashhit.Tpo .deps/libsgm_a-hashhit.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-menu.o -MD -MP -MF .deps/smalt-menu.Tpo -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.c
mv -f .deps/libsgm_a-hashidx.Tpo .deps/libsgm_a-hashidx.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-threads.o -MD -MP -MF .deps/smalt-threads.Tpo -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.c
mv -f .deps/libsgm_a-segment.Tpo .deps/libsgm_a-segment.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-infmt.o -MD -MP -MF .deps/smalt-infmt.Tpo -c -o smalt-infmt.o `test -f 'infmt.c' || echo './'`infmt.c
mv -f .deps/smalt-infmt.Tpo .deps/smalt-infmt.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-results.o -MD -MP -MF .deps/smalt-results.Tpo -c -o smalt-results.o `test -f 'results.c' || echo './'`results.c
mv -f .deps/smalt-threads.Tpo .deps/smalt-threads.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-resultpairs.o -MD -MP -MF .deps/smalt-resultpairs.Tpo -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.c
results.c: In function 'resultSetInferInsertSize':
results.c:2470:11: warning: self-comparison always evaluates to true [-Wtautological-compare]
rp->sidx == rp->sidx) {
^~
mv -f .deps/smalt-smalt.Tpo .deps/smalt-smalt.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-report.o -MD -MP -MF .deps/smalt-report.Tpo -c -o smalt-report.o `test -f 'report.c' || echo './'`report.c
mv -f .deps/smalt-menu.Tpo .deps/smalt-menu.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-rmap.o -MD -MP -MF .deps/smalt-rmap.Tpo -c -o smalt-rmap.o `test -f 'rmap.c' || echo './'`rmap.c
mv -f .deps/smalt-resultpairs.Tpo .deps/smalt-resultpairs.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-insert.o -MD -MP -MF .deps/smalt-insert.Tpo -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c
mv -f .deps/smalt-insert.Tpo .deps/smalt-insert.Po
rm -f libseq.a
ar cru libseq.a elib.o filio.o sequence.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libseq.a
rm -f libsgm.a
ar cru libsgm.a libsgm_a-score.o libsgm_a-diffstr.o libsgm_a-alibuffer.o libsgm_a-alignment.o libsgm_a-sort.o libsgm_a-array.o libsgm_a-interval.o libsgm_a-hashidx.o libsgm_a-hashhit.o libsgm_a-segment.o libseq.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libsgm.a
mv -f .deps/smalt-report.Tpo .deps/smalt-report.Po
mv -f .deps/smalt-rmap.Tpo .deps/smalt-rmap.Po
mv -f .deps/smalt-results.Tpo .deps/smalt-results.Po
gcc -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o smalt smalt-smalt.o smalt-menu.o smalt-threads.o smalt-infmt.o smalt-results.o smalt-resultpairs.o smalt-report.o smalt-rmap.o smalt-insert.o libsgm.a libseq.a -lbambamc -lz -lm -lpthread -lz
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making all in test
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
make[4]: Entering directory '/<<PKGBUILDDIR>>/test'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
Making all in misc
make[3]: Entering directory '/<<PKGBUILDDIR>>/misc'
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT simread.o -MD -MP -MF .deps/simread.Tpo -c -o simread.o simread.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT rsample.o -MD -MP -MF .deps/rsample.Tpo -c -o rsample.o rsample.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT fetchseq.o -MD -MP -MF .deps/fetchseq.Tpo -c -o fetchseq.o fetchseq.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT splitreads.o -MD -MP -MF .deps/splitreads.Tpo -c -o splitreads.o splitreads.c
mv -f .deps/rsample.Tpo .deps/rsample.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT mixreads.o -MD -MP -MF .deps/mixreads.Tpo -c -o mixreads.o mixreads.c
mv -f .deps/splitreads.Tpo .deps/splitreads.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT splitmates.o -MD -MP -MF .deps/splitmates.Tpo -c -o splitmates.o splitmates.c
mv -f .deps/fetchseq.Tpo .deps/fetchseq.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT readstats.o -MD -MP -MF .deps/readstats.Tpo -c -o readstats.o readstats.c
simread.c: In function 'simulateSingleRead':
simread.c:534:49: warning: '%s' directive writing up to 4095 bytes into a region of size between 3815 and 4070 [-Wformat-overflow=]
sprintf(read_name, "%s_%9.9i_%s_%9.9u_%lli_%c_%s", readnamprefix, readnum,
^~
refnamp, so+1, (long long signed) sidx, (is_reverse)? 'R':'F', alistr);
~~~~~~
In file included from /usr/include/stdio.h:862,
from simread.c:29:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output 27 or more bytes (assuming 4377) into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
simread.c:534:49: warning: '%s' directive writing up to 4095 bytes into a region of size between 3815 and 4070 [-Wformat-overflow=]
sprintf(read_name, "%s_%9.9i_%s_%9.9u_%lli_%c_%s", readnamprefix, readnum,
^~
refnamp, so+1, (long long signed) sidx, (is_reverse)? 'R':'F', alistr);
~~~~~~
In file included from /usr/include/stdio.h:862,
from simread.c:29:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output 27 or more bytes (assuming 4377) into a destination of size 4096
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mv -f .deps/readstats.Tpo .deps/readstats.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT trunkreads.o -MD -MP -MF .deps/trunkreads.Tpo -c -o trunkreads.o trunkreads.c
mv -f .deps/splitmates.Tpo .deps/splitmates.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT basqcol.o -MD -MP -MF .deps/basqcol.Tpo -c -o basqcol.o basqcol.c
mv -f .deps/trunkreads.Tpo .deps/trunkreads.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT basqual.o -MD -MP -MF .deps/basqual.Tpo -c -o basqual.o basqual.c
mv -f .deps/mixreads.Tpo .deps/mixreads.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT simqual.o -MD -MP -MF .deps/simqual.Tpo -c -o simqual.o simqual.c
mv -f .deps/basqcol.Tpo .deps/basqcol.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT diffstr.o -MD -MP -MF .deps/diffstr.Tpo -c -o diffstr.o `test -f '../src/diffstr.c' || echo './'`../src/diffstr.c
mv -f .deps/simqual.Tpo .deps/simqual.Po
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fetchseq fetchseq.o ../src/libseq.a -lz
mv -f .deps/basqual.Tpo .deps/basqual.Po
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitreads splitreads.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mixreads mixreads.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitmates splitmates.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o readstats readstats.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o trunkreads trunkreads.o ../src/libseq.a -lz
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o basqcol basqcol.o basqual.o ../src/libseq.a -lz
mv -f .deps/simread.Tpo .deps/simread.Po
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simread simread.o rsample.o ../src/libsgm.a ../src/libseq.a -lm -lz
mv -f .deps/diffstr.Tpo .deps/diffstr.Po
gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simqual simqual.o basqual.o diffstr.o ../src/libseq.a -lm -lz
make[3]: Leaving directory '/<<PKGBUILDDIR>>/misc'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making check in test
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
make sequenceReverseComplement_test smalt_Xali_test
make[4]: Entering directory '/<<PKGBUILDDIR>>/test'
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT sequenceReverseComplement_test.o -MD -MP -MF .deps/sequenceReverseComplement_test.Tpo -c -o sequenceReverseComplement_test.o sequenceReverseComplement_test.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-smalt.o -MD -MP -MF .deps/smalt_Xali_test-smalt.Tpo -c -o smalt_Xali_test-smalt.o `test -f '../src/smalt.c' || echo './'`../src/smalt.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-menu.o -MD -MP -MF .deps/smalt_Xali_test-menu.Tpo -c -o smalt_Xali_test-menu.o `test -f '../src/menu.c' || echo './'`../src/menu.c
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-threads.o -MD -MP -MF .deps/smalt_Xali_test-threads.Tpo -c -o smalt_Xali_test-threads.o `test -f '../src/threads.c' || echo './'`../src/threads.c
../src/smalt.c: In function 'cleanupSmaltOutput':
../src/smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter]
static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op)
~~~~~~~~^~~~~~~
mv -f .deps/sequenceReverseComplement_test.Tpo .deps/sequenceReverseComplement_test.Po
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-infmt.o -MD -MP -MF .deps/smalt_Xali_test-infmt.Tpo -c -o smalt_Xali_test-infmt.o `test -f '../src/infmt.c' || echo './'`../src/infmt.c
mv -f .deps/smalt_Xali_test-infmt.Tpo .deps/smalt_Xali_test-infmt.Po
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-results.o -MD -MP -MF .deps/smalt_Xali_test-results.Tpo -c -o smalt_Xali_test-results.o `test -f '../src/results.c' || echo './'`../src/results.c
mv -f .deps/smalt_Xali_test-threads.Tpo .deps/smalt_Xali_test-threads.Po
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-resultpairs.o -MD -MP -MF .deps/smalt_Xali_test-resultpairs.Tpo -c -o smalt_Xali_test-resultpairs.o `test -f '../src/resultpairs.c' || echo './'`../src/resultpairs.c
../src/results.c: In function 'resultSetInferInsertSize':
../src/results.c:2470:11: warning: self-comparison always evaluates to true [-Wtautological-compare]
rp->sidx == rp->sidx) {
^~
mv -f .deps/smalt_Xali_test-smalt.Tpo .deps/smalt_Xali_test-smalt.Po
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-insert.o -MD -MP -MF .deps/smalt_Xali_test-insert.Tpo -c -o smalt_Xali_test-insert.o `test -f '../src/insert.c' || echo './'`../src/insert.c
mv -f .deps/smalt_Xali_test-menu.Tpo .deps/smalt_Xali_test-menu.Po
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-report.o -MD -MP -MF .deps/smalt_Xali_test-report.Tpo -c -o smalt_Xali_test-report.o `test -f '../src/report.c' || echo './'`../src/report.c
mv -f .deps/smalt_Xali_test-resultpairs.Tpo .deps/smalt_Xali_test-resultpairs.Po
gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-rmap.o -MD -MP -MF .deps/smalt_Xali_test-rmap.Tpo -c -o smalt_Xali_test-rmap.o `test -f '../src/rmap.c' || echo './'`../src/rmap.c
mv -f .deps/smalt_Xali_test-insert.Tpo .deps/smalt_Xali_test-insert.Po
gcc -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o sequenceReverseComplement_test sequenceReverseComplement_test.o ../src/libseq.a -lz
mv -f .deps/smalt_Xali_test-rmap.Tpo .deps/smalt_Xali_test-rmap.Po
mv -f .deps/smalt_Xali_test-report.Tpo .deps/smalt_Xali_test-report.Po
mv -f .deps/smalt_Xali_test-results.Tpo .deps/smalt_Xali_test-results.Po
gcc -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o smalt_Xali_test smalt_Xali_test-smalt.o smalt_Xali_test-menu.o smalt_Xali_test-threads.o smalt_Xali_test-infmt.o smalt_Xali_test-results.o smalt_Xali_test-resultpairs.o smalt_Xali_test-insert.o smalt_Xali_test-report.o smalt_Xali_test-rmap.o ../src/libsgm.a ../src/libseq.a -lbambamc -lz -lm -lpthread -lz
make[4]: Leaving directory '/<<PKGBUILDDIR>>/test'
make check-TESTS
make[4]: Entering directory '/<<PKGBUILDDIR>>/test'
PASS: splitReads_test.py
PASS: results_split_test.py
PASS: ouform_cigar_test.py
PASS: sample_test.py
PASS: cigar_test.py
PASS: mthread_test.py
PASS: ioform_test.py
PASS: xali_test.py
PASS: bam_cigar_test.py
==================
All 9 tests passed
==================
make[4]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
Making check in misc
make[2]: Entering directory '/<<PKGBUILDDIR>>/misc'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/misc'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# upstream install does install more files than needed
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/smalt/usr/lib/smalt/test/sequenceReverseComplement_test debian/smalt/usr/bin/smalt 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 'smalt' in '../smalt_0.7.6-8_armhf.deb'.
dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-8_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../smalt_0.7.6-8_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build smalt-0.7.6
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-10-27T05:25:30Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
smalt_0.7.6-8_armhf.changes:
----------------------------
Format: 1.8
Date: Wed, 24 Oct 2018 21:08:08 +0200
Source: smalt
Binary: smalt smalt-examples
Architecture: armhf
Version: 0.7.6-8
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
smalt - Sequence Mapping and Alignment Tool
smalt-examples - Sequence Mapping and Alignment Tool (examples)
Changes:
smalt (0.7.6-8) unstable; urgency=medium
.
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Do not autoreconf since config is broken
Checksums-Sha1:
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fb26808defd951fb70010de9be19070f6b17ec6d 5846 smalt_0.7.6-8_armhf.buildinfo
f6dbaf30cfdc7108d4863054644fbcc4ba013b68 93164 smalt_0.7.6-8_armhf.deb
Checksums-Sha256:
50a813ec746363a4f1dbea894acf2fe9dbdbd583b3adffb2baf4692cd62e65cb 367664 smalt-dbgsym_0.7.6-8_armhf.deb
5e2f14912fcaacc6035e274fb6317e6479dbafcf15e40c7fdc7a23a3691e2d79 5846 smalt_0.7.6-8_armhf.buildinfo
93b0aec8085dfdeed1fd79e6f61f471eb972ed6de6c04cfb81f12a68f6002595 93164 smalt_0.7.6-8_armhf.deb
Files:
c6df6883d2e73ea66aa8387e5f599d5d 367664 debug optional smalt-dbgsym_0.7.6-8_armhf.deb
2d78c18a374260eae88c028333c9cb72 5846 science optional smalt_0.7.6-8_armhf.buildinfo
97b9517d36814161ec35d13913ef3fe7 93164 science optional smalt_0.7.6-8_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
smalt-dbgsym_0.7.6-8_armhf.deb
------------------------------
new Debian package, version 2.0.
size 367664 bytes: control archive=596 bytes.
403 bytes, 12 lines control
212 bytes, 2 lines md5sums
Package: smalt-dbgsym
Source: smalt
Version: 0.7.6-8
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 407
Depends: smalt (= 0.7.6-8)
Section: debug
Priority: optional
Description: debug symbols for smalt
Build-Ids: 199a0a75a719d8ec200f4a76bedccfb9ac5bd6cd 752532dcb548a313802afa2d6b3a4d4939062d56
drwxr-xr-x root/root 0 2018-10-24 19:08 ./
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/lib/debug/.build-id/19/
-rw-r--r-- root/root 339564 2018-10-24 19:08 ./usr/lib/debug/.build-id/19/9a0a75a719d8ec200f4a76bedccfb9ac5bd6cd.debug
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/lib/debug/.build-id/75/
-rw-r--r-- root/root 64832 2018-10-24 19:08 ./usr/lib/debug/.build-id/75/2532dcb548a313802afa2d6b3a4d4939062d56.debug
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/share/
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-10-24 19:08 ./usr/share/doc/smalt-dbgsym -> smalt
smalt_0.7.6-8_armhf.deb
-----------------------
new Debian package, version 2.0.
size 93164 bytes: control archive=1220 bytes.
1293 bytes, 30 lines control
334 bytes, 5 lines md5sums
Package: smalt
Version: 0.7.6-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 248
Depends: libbambamc0, libc6 (>= 2.7), zlib1g (>= 1:1.2.0.2)
Section: science
Priority: optional
Homepage: http://www.sanger.ac.uk/science/tools/smalt-0
Description: Sequence Mapping and Alignment Tool
SMALT efficiently aligns DNA sequencing reads with a reference genome.
Reads from a wide range of sequencing platforms, for example Illumina,
Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including
paired reads.
.
The software employs a perfect hash index of short words (< 20
nucleotides long), sampled at equidistant steps along the genomic
reference sequences.
.
For each read, potentially matching segments in the reference are
identified from seed matches in the index and subsequently aligned with
the read using a banded Smith-Waterman algorithm.
.
The best gapped alignments of each read is reported including a score
for the reliability of the best mapping. The user can adjust the
trade-off between sensitivity and speed by tuning the length and spacing
of the hashed words.
.
A mode for the detection of split (chimeric) reads is provided.
Multi-threaded program execution is supported.
drwxr-xr-x root/root 0 2018-10-24 19:08 ./
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/bin/
-rwxr-xr-x root/root 194004 2018-10-24 19:08 ./usr/bin/smalt
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/lib/
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/lib/smalt/
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/lib/smalt/test/
-rwxr-xr-x root/root 42452 2018-10-24 19:08 ./usr/lib/smalt/test/sequenceReverseComplement_test
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/share/
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/share/doc/smalt/
-rw-r--r-- root/root 988 2018-10-24 19:08 ./usr/share/doc/smalt/changelog.Debian.gz
-rw-r--r-- root/root 1182 2018-10-24 19:08 ./usr/share/doc/smalt/copyright
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/share/man/
drwxr-xr-x root/root 0 2018-10-24 19:08 ./usr/share/man/man1/
-rw-r--r-- root/root 884 2018-10-24 19:08 ./usr/share/man/man1/smalt.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 81760
Build-Time: 1841
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 416
Job: smalt_0.7.6-8
Machine Architecture: armhf
Package: smalt
Package-Time: 2319
Source-Version: 0.7.6-8
Space: 81760
Status: successful
Version: 0.7.6-8
--------------------------------------------------------------------------------
Finished at 2018-10-27T05:25:30Z
Build needed 00:38:39, 81760k disc space