smalt →
0.7.6-7 →
armhf → 2018-03-13 15:31:42
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| smalt 0.7.6-7 (armhf) Tue, 13 Mar 2018 14:49:42 +0000 |
+==============================================================================+
Package: smalt
Version: 0.7.6-7
Source Version: 0.7.6-7
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-bd4bc3bc-29bf-4d72-8d17-3e868a9f490c' 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 [10.6 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.4 MB]
Fetched 23.1 MB in 27s (840 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://anonscm.debian.org/git/debian-med/smalt.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/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 0.7.6-7 (dsc) [2078 B]
Get:2 http://172.17.0.1/private buster-staging/main smalt 0.7.6-7 (tar) [72.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main smalt 0.7.6-7 (diff) [4864 B]
Fetched 72.3 MB in 8s (9631 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/smalt-etseDg/smalt-0.7.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/smalt-etseDg' 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-xfLlVq/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-xfLlVq/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-xfLlVq/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-xfLlVq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-xfLlVq/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-xfLlVq/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-xfLlVq/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-xfLlVq/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2834 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 NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 89 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-xfLlVq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (20.7 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13255 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 (>= 9.20160114), zlib1g-dev, python, samtools, libbambamc-dev
Filtered Build-Depends: debhelper (>= 9.20160114), zlib1g-dev, python, samtools, libbambamc-dev
dpkg-deb: building package 'sbuild-build-depends-smalt-dummy' in '/<<BUILDDIR>>/resolver-xfLlVq/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-xfLlVq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-xfLlVq/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-xfLlVq/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-xfLlVq/apt_archive ./ Sources [519 B]
Get:5 copy:/<<BUILDDIR>>/resolver-xfLlVq/apt_archive ./ Packages [599 B]
Fetched 2451 B in 1s (3432 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 additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbambamc-dev libbambamc0 libbsd0
libcroco3 libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl
libgdbm5 libglib2.0-0 libgssapi-krb5-2 libhts2 libicu57 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib librtmp1 libsigsegv2 libssh2-1 libssl1.1
libtimedate-perl libtool libxml2 m4 man-db mime-support pkg-config
po-debconf python python-minimal python2.7 python2.7-minimal samtools
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff
gdbm-l10n krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler
gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python-doc
python-tk python2.7-doc binfmt-support
Recommended packages:
curl | wget | lynx-cur ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales 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 file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbambamc-dev libbambamc0 libbsd0
libcroco3 libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl
libgdbm5 libglib2.0-0 libgssapi-krb5-2 libhts2 libicu57 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib librtmp1 libsigsegv2 libssh2-1 libssl1.1
libtimedate-perl libtool libxml2 m4 man-db mime-support pkg-config
po-debconf python python-minimal python2.7 python2.7-minimal samtools
sbuild-build-depends-smalt-dummy zlib1g-dev
0 upgraded, 57 newly installed, 0 to remove and 89 not upgraded.
Need to get 24.7 MB/25.9 MB of archives.
After this operation, 87.6 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-xfLlVq/apt_archive ./ sbuild-build-depends-smalt-dummy 0.invalid.0 [888 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.7-1 [96.8 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 libgdbm5 armhf 1.14.1-4 [54.0 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.2-1 [1145 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.14-6 [393 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.14-6 [1080 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.14-4 [41.0 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.14-6 [1841 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.14-6 [293 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.14-4 [20.4 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.14-4 [155 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-2 [225 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-2 [105 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-2 [63.8 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9.2 [12.1 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-1 [32.2 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 16 [16.3 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.3-2 [2651 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-8 [7411 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-6.1 [602 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-2 [132 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.1.5 [1007 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libbambamc0 armhf 0.0.50-1 [30.3 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf pkg-config armhf 0.29-4 [59.2 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libbambamc-dev armhf 0.0.50-1 [39.4 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.16-2 [59.0 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.16-2 [116 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.16-2 [265 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.16-2 [135 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.31.0-1 [70.1 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.19.1-5 [43.7 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.58.0-2 [275 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 1.7-1 [248 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libbambamc0.
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Unpacking libbambamc0 (0.0.50-1) ...
Selecting previously unselected package pkg-config.
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Unpacking pkg-config (0.29-4) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../28-zlib1g-dev_1%3a1.2.8.dfsg-5_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Selecting previously unselected package libbambamc-dev.
Preparing to unpack .../29-libbambamc-dev_0.0.50-1_armhf.deb ...
Unpacking libbambamc-dev (0.0.50-1) ...
Selecting previously unselected package libkrb5support0:armhf.
Preparing to unpack .../30-libkrb5support0_1.16-2_armhf.deb ...
Unpacking libkrb5support0:armhf (1.16-2) ...
Selecting previously unselected package libk5crypto3:armhf.
Preparing to unpack .../31-libk5crypto3_1.16-2_armhf.deb ...
Unpacking libk5crypto3:armhf (1.16-2) ...
Selecting previously unselected package libkrb5-3:armhf.
Preparing to unpack .../32-libkrb5-3_1.16-2_armhf.deb ...
Unpacking libkrb5-3:armhf (1.16-2) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
Preparing to unpack .../33-libgssapi-krb5-2_1.16-2_armhf.deb ...
Unpacking libgssapi-krb5-2:armhf (1.16-2) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../34-libnghttp2-14_1.31.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.31.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../35-libpsl5_0.19.1-5_armhf.deb ...
Unpacking libpsl5:armhf (0.19.1-5) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../36-librtmp1_2.4+20151223.gitfa8646d.1-1_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../37-libssh2-1_1.8.0-1_armhf.deb ...
Unpacking libssh2-1:armhf (1.8.0-1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../38-libcurl3-gnutls_7.58.0-2_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.58.0-2) ...
Selecting previously unselected package libhts2:armhf.
Preparing to unpack .../39-libhts2_1.7-2_armhf.deb ...
Unpacking libhts2:armhf (1.7-2) ...
Selecting previously unselected package samtools.
Preparing to unpack .../40-samtools_1.7-1_armhf.deb ...
Unpacking samtools (1.7-1) ...
Selecting previously unselected package sbuild-build-depends-smalt-dummy.
Preparing to unpack .../41-sbuild-build-depends-smalt-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-smalt-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.2.5-3) ...
Setting up libarchive-zip-perl (1.60-1) ...
Setting up libnghttp2-14:armhf (1.31.0-1) ...
Setting up mime-support (3.60) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.12-1) ...
Setting up libpsl5:armhf (0.19.1-5) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.54.3-2) ...
No schema files found: doing nothing.
Setting up gettext-base (0.19.8.1-4) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libgdbm5:armhf (1.14.1-4) ...
Setting up libicu57:armhf (57.1-8) ...
Setting up libbsd0:armhf (0.8.7-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-6.1) ...
Setting up libmagic-mgc (1:5.32-2) ...
Setting up libmagic1:armhf (1:5.32-2) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up pkg-config (0.29-4) ...
Setting up libssh2-1:armhf (1.8.0-1) ...
Processing triggers for libc-bin (2.26-4+rpi1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libssl1.1:armhf (1.1.0g-2) ...
Setting up libbambamc0 (0.0.50-1) ...
Setting up libkeyutils1:armhf (1.5.9-9.2) ...
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 (2.7.14-6) ...
Setting up autopoint (0.19.8.1-4) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.040-1) ...
Setting up gettext (0.19.8.1-4) ...
Setting up python2.7 (2.7.14-6) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-2) ...
Setting up libkrb5support0:armhf (1.16-2) ...
Setting up libpython-stdlib:armhf (2.7.14-4) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libbambamc-dev (0.0.50-1) ...
Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python (2.7.14-4) ...
Setting up libtool (2.4.6-2) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up libcurl3-gnutls:armhf (7.58.0-2) ...
Setting up libhts2:armhf (1.7-2) ...
Setting up samtools (1.7-1) ...
Setting up dh-autoreconf (16) ...
Setting up debhelper (11.1.5) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Setting up sbuild-build-depends-smalt-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.26-4+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_2.29.1-13+rpi1 dpkg-dev_1.19.0.5 g++-7_7.2.0-19+b1 gcc-7_7.2.0-19+b1 libc6-dev_2.26-4+rpi1 libstdc++-7-dev_7.2.0-19+b1 libstdc++6_7.2.0-19+b1 linux-libc-dev_4.9.51-1+rpi3+b1
Package versions: adduser_3.116 apt_1.6~alpha6 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-13+rpi1 binutils-arm-linux-gnueabihf_2.29.1-13+rpi1 binutils-common_2.29.1-13+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.30.2-0.3 build-essential_12.4 bzip2_1.0.6-8.1 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-19+b1 dash_0.5.8-2.10 debconf_1.5.65 debhelper_11.1.5 debianutils_4.8.4 dh-autoreconf_16 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.4-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.43.8-2 e2fsprogs_1.43.8-2 fakeroot_1.22-2 fdisk_2.30.2-0.3 file_1:5.32-2 findutils_4.6.0+git+20170828-2 g++_4:7.2.0-1d1 g++-7_7.2.0-19+b1 gcc_4:7.2.0-1d1 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_4.9.3-14 gcc-5-base_5.4.1-4 gcc-6-base_6.4.0-11 gcc-7_7.2.0-19+b1 gcc-7-base_7.2.0-19+b1 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.4-1 gnupg-l10n_2.2.4-1 gnupg-utils_2.2.4-1 gpg_2.2.4-1 gpg-agent_2.2.4-1 gpg-wks-client_2.2.4-1 gpg-wks-server_2.2.4-1 gpgconf_2.2.4-1 gpgsm_2.2.4-1 gpgv_2.2.4-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-2 libapt-pkg5.0_1.6~alpha6 libarchive-zip-perl_1.60-1 libasan4_7.2.0-19+b1 libassuan0_2.5.1-1 libatomic1_7.2.0-19+b1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbambamc-dev_0.0.50-1 libbambamc0_0.0.50-1 libbinutils_2.29.1-13+rpi1 libblkid1_2.30.2-0.3 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.26-4+rpi1 libc-dev-bin_2.26-4+rpi1 libc6_2.26-4+rpi1 libc6-dev_2.26-4+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_7.2.0-19+b1 libcilkrts5_7.2.0-19+b1 libcomerr2_1.43.8-2 libcroco3_0.6.12-2 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.58.0-2 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.2-1 libdebconfclient0_0.239 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.89-1+rpi1 libdrm2_2.4.89-1+rpi1 libexpat1_2.2.5-3 libfakeroot_1.22-2 libfdisk1_2.30.2-0.3 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-19+b1 libgcc1_1:7.2.0-19+b1 libgcrypt20_1.8.1-4 libgdbm3_1.8.3-14 libgdbm5_1.14.1-4 libglib2.0-0_2.54.3-2 libgmp10_2:6.1.2+dfsg-2 libgnutls30_3.5.17-1 libgomp1_7.2.0-19+b1 libgpg-error0_1.27-5 libgssapi-krb5-2_1.16-2 libhogweed4_3.4-1 libhts2_1.7-2 libicu57_57.1-8 libidn11_1.33-2.1 libidn2-0_2.0.4-1.1 libip4tc0_1.6.1-2+b1 libisl15_0.18-1 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-2 libmagic1_1:5.32-2 libmount1_2.30.2-0.3 libmpc3_1.1.0-1 libmpfr6_4.0.0-7 libncurses5_6.0+20171125-1 libncursesw5_6.0+20171125-1 libnettle6_3.4-1 libnghttp2-14_1.31.0-1 libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-8 libperl5.26_5.26.1-4 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3 libpsl5_0.19.1-5 libpython-stdlib_2.7.14-4 libpython2.7-minimal_2.7.14-6 libpython2.7-stdlib_2.7.14-6 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-1 libsmartcols1_2.30.2-0.3 libsqlite3-0_3.22.0-1 libss2_1.43.8-2 libssh2-1_1.8.0-1 libssl1.1_1.1.0g-2 libstdc++-7-dev_7.2.0-19+b1 libstdc++6_7.2.0-19+b1 libsystemd0_236-2 libtasn1-6_4.13-2 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20171125-1 libtool_2.4.6-2 libubsan0_7.2.0-19+b1 libudev1_236-2 libunistring2_0.9.8-1 libuuid1_2.30.2-0.3 libxml2_2.9.4+dfsg1-6.1 linux-base_4.5 linux-libc-dev_4.9.51-1+rpi3+b1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.2-1 mawk_1.3.3-17 mime-support_3.60 mount_2.30.2-0.3 multiarch-support_2.26-4+rpi1 nano_2.9.2-1 ncurses-base_6.0+20171125-1 ncurses-bin_6.0+20171125-1 passwd_1:4.5-1 patch_2.7.5-1 perl_5.26.1-4 perl-base_5.26.1-4 perl-modules-5.26_5.26.1-4 pinentry-curses_1.0.0-3 pkg-config_0.29-4 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.14-4 python-minimal_2.7.14-4 python2.7_2.7.14-6 python2.7-minimal_2.7.14-6 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 samtools_1.7-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-smalt-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.11 systemd_236-2 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018c-1 udev_236-2 util-linux_2.30.2-0.3 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Nov 20 11:46:39 2017 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_0.7.6-7.dsc
dpkg-source: info: extracting smalt in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking smalt_0.7.6.orig.tar.gz
dpkg-source: info: unpacking smalt_0.7.6-7.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-bd4bc3bc-29bf-4d72-8d17-3e868a9f490c
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 0.7.6-7
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 # this fails because auf broken upstream autoconf stuff: - - with autoreconf
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 # this fails because auf broken upstream autoconf stuff: - - with autoreconf
dh_update_autotools_config -a
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 -j1
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
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 filio.o -MD -MP -MF .deps/filio.Tpo -c -o filio.o filio.c
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 sequence.o -MD -MP -MF .deps/sequence.Tpo -c -o sequence.o sequence.c
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/sequence.Tpo .deps/sequence.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
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 */
^~~~~~
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-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-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-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/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-alignment.o -MD -MP -MF .deps/libsgm_a-alignment.Tpo -c -o libsgm_a-alignment.o `test -f 'alignment.c' || echo './'`alignment.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-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-sort.o -MD -MP -MF .deps/libsgm_a-sort.Tpo -c -o libsgm_a-sort.o `test -f 'sort.c' || echo './'`sort.c
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-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-hashidx.o -MD -MP -MF .deps/libsgm_a-hashidx.Tpo -c -o libsgm_a-hashidx.o `test -f 'hashidx.c' || echo './'`hashidx.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";
^~~~~~~~~~~~~~~~~~~~~
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 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-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 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
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/libsgm_a-segment.Tpo .deps/libsgm_a-segment.Po
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
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/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-menu.o -MD -MP -MF .deps/smalt-menu.Tpo -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.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-threads.o -MD -MP -MF .deps/smalt-threads.Tpo -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.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-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
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-results.Tpo .deps/smalt-results.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
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-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-report.Tpo .deps/smalt-report.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-rmap.Tpo .deps/smalt-rmap.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
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
mv -f .deps/simread.Tpo .deps/simread.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 rsample.o -MD -MP -MF .deps/rsample.Tpo -c -o rsample.o rsample.c
mv -f .deps/rsample.Tpo .deps/rsample.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
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
mv -f .deps/fetchseq.Tpo .deps/fetchseq.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
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/splitreads.Tpo .deps/splitreads.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 -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/mixreads.Tpo .deps/mixreads.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 mixreads mixreads.o ../src/libseq.a -lz
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/splitmates.Tpo .deps/splitmates.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 splitmates splitmates.o ../src/libseq.a -lz
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
mv -f .deps/readstats.Tpo .deps/readstats.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 readstats readstats.o ../src/libseq.a -lz
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/trunkreads.Tpo .deps/trunkreads.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 trunkreads trunkreads.o ../src/libseq.a -lz
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/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 basqual.o -MD -MP -MF .deps/basqual.Tpo -c -o basqual.o basqual.c
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 basqcol basqcol.o basqual.o ../src/libseq.a -lz
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/simqual.Tpo .deps/simqual.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/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 -j1 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
mv -f .deps/sequenceReverseComplement_test.Tpo .deps/sequenceReverseComplement_test.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
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
../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/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-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
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-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
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-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
../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-results.Tpo .deps/smalt_Xali_test-results.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
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-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-insert.Tpo .deps/smalt_Xali_test-insert.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-report.Tpo .deps/smalt_Xali_test-report.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-rmap.Tpo .deps/smalt_Xali_test-rmap.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>>'
fakeroot debian/rules binary-arch
dh binary-arch # this fails because auf broken upstream autoconf stuff: - - with autoreconf
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-dbgsym' in '../smalt-dbgsym_0.7.6-7_armhf.deb'.
dpkg-deb: building package 'smalt' in '../smalt_0.7.6-7_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../smalt_0.7.6-7_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 2018-03-13T15:31:06Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
smalt_0.7.6-7_armhf.changes:
----------------------------
Format: 1.8
Date: Mon, 20 Nov 2017 12:41:33 +0100
Source: smalt
Binary: smalt smalt-examples
Architecture: armhf
Version: 0.7.6-7
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 (0.7.6-7) unstable; urgency=medium
.
* Moved packaging from SVN to Git
* drop "Testsuite: autopkgtest" from d/control
* Remark: since autoreconf does not work the package was not switched to
debhelper 10
* Standards-Version: 4.1.1
* Remove unused lintian-override
* debhelper tools from autotools-dev has been replaced by the tool
dh_update_autotools_config
Checksums-Sha1:
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9c6359cb71a6ad543e26b890bad5e1620b1e910b 5561 smalt_0.7.6-7_armhf.buildinfo
ec2659450c46de73df2be51d08ea8a8836c91ec5 92596 smalt_0.7.6-7_armhf.deb
Checksums-Sha256:
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c770980cf649bdea2600e9bc48397461e63dcd19b180f5c5a32bc1c3d49688a1 5561 smalt_0.7.6-7_armhf.buildinfo
2a256ee5cc43efef9c9058426dd856558fd5652862971e0d11aed136c49111b6 92596 smalt_0.7.6-7_armhf.deb
Files:
835f20192a4fa532f5ce8f2cd98d3ec1 294092 debug optional smalt-dbgsym_0.7.6-7_armhf.deb
4339e72c2393e26fe5a3beae2ba865c9 5561 science optional smalt_0.7.6-7_armhf.buildinfo
b49ff7d00df12511444bf1fb384c7962 92596 science optional smalt_0.7.6-7_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
smalt-dbgsym_0.7.6-7_armhf.deb
------------------------------
new Debian package, version 2.0.
size 294092 bytes: control archive=592 bytes.
403 bytes, 12 lines control
212 bytes, 2 lines md5sums
Package: smalt-dbgsym
Source: smalt
Version: 0.7.6-7
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 335
Depends: smalt (= 0.7.6-7)
Section: debug
Priority: optional
Description: debug symbols for smalt
Build-Ids: 2f0a65e65128a5d473cc042f49268df4d7272270 4c47576f7194b5ad320aa160bacadf991a863181
drwxr-xr-x root/root 0 2017-11-20 11:41 ./
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/lib/
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/lib/debug/.build-id/2f/
-rw-r--r-- root/root 277896 2017-11-20 11:41 ./usr/lib/debug/.build-id/2f/0a65e65128a5d473cc042f49268df4d7272270.debug
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/lib/debug/.build-id/4c/
-rw-r--r-- root/root 53220 2017-11-20 11:41 ./usr/lib/debug/.build-id/4c/47576f7194b5ad320aa160bacadf991a863181.debug
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/share/
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-11-20 11:41 ./usr/share/doc/smalt-dbgsym -> smalt
smalt_0.7.6-7_armhf.deb
-----------------------
new Debian package, version 2.0.
size 92596 bytes: control archive=1220 bytes.
1293 bytes, 30 lines control
334 bytes, 5 lines md5sums
Package: smalt
Version: 0.7.6-7
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 240
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 2017-11-20 11:41 ./
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/bin/
-rwxr-xr-x root/root 189908 2017-11-20 11:41 ./usr/bin/smalt
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/lib/
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/lib/smalt/
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/lib/smalt/test/
-rwxr-xr-x root/root 38356 2017-11-20 11:41 ./usr/lib/smalt/test/sequenceReverseComplement_test
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/share/
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/share/doc/smalt/
-rw-r--r-- root/root 921 2017-11-20 11:41 ./usr/share/doc/smalt/changelog.Debian.gz
-rw-r--r-- root/root 1182 2017-11-20 11:41 ./usr/share/doc/smalt/copyright
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/share/man/
drwxr-xr-x root/root 0 2017-11-20 11:41 ./usr/share/man/man1/
-rw-r--r-- root/root 884 2017-11-20 11:41 ./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: 80588
Build-Time: 1977
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 441
Job: smalt_0.7.6-7
Machine Architecture: armhf
Package: smalt
Package-Time: 2484
Source-Version: 0.7.6-7
Space: 80588
Status: successful
Version: 0.7.6-7
--------------------------------------------------------------------------------
Finished at 2018-03-13T15:31:06Z
Build needed 00:41:24, 80588k disc space