smalt →
0.7.6-6 →
armhf → 2016-05-29 12:22:57
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on testbuildd.raspbian.org
+==============================================================================+
| smalt 0.7.6-6 (armhf) 29 May 2016 11:42 |
+==============================================================================+
Package: smalt
Version: 0.7.6-6
Source Version: 0.7.6-6
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/smalt-GQoZaD/smalt-0.7.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/smalt-GQoZaD' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-8901f23e-1caf-4a7f-8f25-34cb8189a0d4' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9005 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.0 MB]
Fetched 20.0 MB in 24s (817 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 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/smalt/trunk/
Need to get 72.3 MB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main smalt 0.7.6-6 (dsc) [2059 B]
Get:2 http://172.17.0.1/private stretch-staging/main smalt 0.7.6-6 (tar) [72.3 MB]
Get:3 http://172.17.0.1/private stretch-staging/main smalt 0.7.6-6 (diff) [4892 B]
Fetched 72.3 MB in 27s (2598 kB/s)
Download complete and in download only mode
Check architectures
-------------------
Check dependencies
------------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-bbFS1Z/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-bbFS1Z/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-bbFS1Z/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-bbFS1Z/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-bbFS1Z/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-bbFS1Z/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-bbFS1Z/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-bbFS1Z/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-bbFS1Z/apt_archive ./ Packages [528 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-bbFS1Z/apt_archive/./Release.gpg: Signature by key 085A60275B95EE7E758335885FBC947B34E39F26 uses weak digest algorithm (SHA1)
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 28 not upgraded.
Need to get 0 B/762 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-bbFS1Z/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [762 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
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Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
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Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: debhelper (>= 9), zlib1g-dev, python, samtools, libbambamc-dev, autotools-dev
Filtered Build-Depends: debhelper (>= 9), zlib1g-dev, python, samtools, libbambamc-dev, autotools-dev
dpkg-deb: building package 'sbuild-build-depends-smalt-dummy' in '/<<BUILDDIR>>/resolver-cxQSc3/apt_archive/sbuild-build-depends-smalt-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-cxQSc3/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-cxQSc3/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-cxQSc3/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-cxQSc3/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-cxQSc3/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-cxQSc3/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-cxQSc3/apt_archive ./ Sources [242 B]
Get:5 file:/<<BUILDDIR>>/resolver-cxQSc3/apt_archive ./ Packages [559 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-cxQSc3/apt_archive/./Release.gpg: Signature by key 085A60275B95EE7E758335885FBC947B34E39F26 uses weak digest algorithm (SHA1)
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 libffi6 libfile-stripnondeterminism-perl
libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts1 libicu55
libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2
libmagic1 libnettle6 libnghttp2-14 libp11-kit0 libpipeline1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib librtmp1 libsasl2-2
libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.0.2
libtasn1-6 libtimedate-perl libtool libunistring0 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 gettext-doc libasprintf-dev libgettextpo-dev groff
gnutls-bin krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler
gcj-jdk less www-browser libmail-box-perl python-doc python-tk python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales libsasl2-modules libltdl-dev xml-core
libmail-sendmail-perl
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 libffi6 libfile-stripnondeterminism-perl
libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts1 libicu55
libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2
libmagic1 libnettle6 libnghttp2-14 libp11-kit0 libpipeline1 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib librtmp1 libsasl2-2
libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.0.2
libtasn1-6 libtimedate-perl libtool libunistring0 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, 66 newly installed, 0 to remove and 28 not upgraded.
Need to get 27.4 MB/27.4 MB of archives.
After this operation, 91.8 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-cxQSc3/apt_archive ./ sbuild-build-depends-smalt-dummy 0.invalid.0 [802 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.11-9 [382 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.11-9 [1163 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-1 [40.0 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.1.1-2 [60.2 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.12.2-1 [464 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2h-1 [889 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.11-9 [1817 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.11-9 [271 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-1 [19.5 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-1 [150 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libnettle6 armhf 3.2-1 [202 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libhogweed4 armhf 3.2-1 [126 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libidn11 armhf 1.32-3 [110 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libp11-kit0 armhf 0.23.2-3 [93.3 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libtasn1-6 armhf 4.8-1 [44.1 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libgnutls30 armhf 3.4.12-1 [733 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.13.2+dfsg-5 [56.6 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.13.2+dfsg-5 [110 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.13.2+dfsg-5 [259 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.13.2+dfsg-5 [130 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.26.dfsg1-15 [65.6 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.26.dfsg1-15 [96.7 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.42+dfsg-2+rpi1+b2 [198 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.7-2 [424 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.1-1 [2548 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.57-1 [95.1 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160403 [800 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libbambamc0 armhf 0.0.50-1 [30.3 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf pkg-config armhf 0.29-4 [59.2 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libbambamc-dev armhf 0.0.50-1 [39.4 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.10.0-1 [72.2 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.5.0-2.1 [121 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.47.0-1 [244 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.1-1+rpi1 [215 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf samtools armhf 1.3.1-2 [219 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libgnutls30:armhf (3.4.12-1) ...
Selecting previously unselected package libkeyutils1:armhf.
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Selecting previously unselected package libk5crypto3:armhf.
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Selecting previously unselected package libgssapi-krb5-2:armhf.
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Selecting previously unselected package libsasl2-modules-db:armhf.
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Unpacking libsasl2-2:armhf (2.1.26.dfsg1-15) ...
Selecting previously unselected package libldap-2.4-2:armhf.
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Unpacking libldap-2.4-2:armhf (2.4.42+dfsg-2+rpi1+b2) ...
Selecting previously unselected package libicu55:armhf.
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Unpacking libicu55:armhf (55.1-7) ...
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Unpacking libxml2:armhf (2.9.3+dfsg1-1) ...
Selecting previously unselected package libsigsegv2:armhf.
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Unpacking libsigsegv2:armhf (2.10-5) ...
Selecting previously unselected package m4.
Preparing to unpack .../archives/m4_1.4.17-5_armhf.deb ...
Unpacking m4 (1.4.17-5) ...
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Unpacking automake (1:1.15-4) ...
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Unpacking autopoint (0.19.7-2) ...
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Unpacking libglib2.0-0:armhf (2.48.1-1) ...
Selecting previously unselected package libcroco3:armhf.
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Unpacking libcroco3:armhf (0.6.11-1) ...
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Unpacking gettext (0.19.7-2) ...
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Unpacking intltool-debian (0.35.0+20060710.4) ...
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Unpacking po-debconf (1.0.19) ...
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Unpacking libarchive-zip-perl (1.57-1) ...
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Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
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Unpacking libtimedate-perl (2.3000-2) ...
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Unpacking dh-strip-nondeterminism (0.016-1) ...
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Unpacking libtool (2.4.6-0.1) ...
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Unpacking dh-autoreconf (12) ...
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Unpacking debhelper (9.20160403) ...
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Unpacking libbambamc0 (0.0.50-1) ...
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Unpacking pkg-config (0.29-4) ...
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Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package libbambamc-dev.
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Unpacking libbambamc-dev (0.0.50-1) ...
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Unpacking libnghttp2-14:armhf (1.10.0-1) ...
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Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Selecting previously unselected package libssh2-1:armhf.
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Unpacking libssh2-1:armhf (1.5.0-2.1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
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Unpacking libcurl3-gnutls:armhf (7.47.0-1) ...
Selecting previously unselected package libhts1:armhf.
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Unpacking libhts1:armhf (1.3.1-1+rpi1) ...
Selecting previously unselected package samtools.
Preparing to unpack .../samtools_1.3.1-2_armhf.deb ...
Unpacking samtools (1.3.1-2) ...
Selecting previously unselected package sbuild-build-depends-smalt-dummy.
Preparing to unpack .../sbuild-build-depends-smalt-dummy.deb ...
Unpacking sbuild-build-depends-smalt-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.22-7) ...
Setting up groff-base (1.22.3-7) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up bsdmainutils (9.0.10) ...
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 libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up mime-support (3.60) ...
Setting up libexpat1:armhf (2.1.1-2) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up libsqlite3-0:armhf (3.12.2-1) ...
Setting up libssl1.0.2:armhf (1.0.2h-1) ...
Setting up libpython2.7-stdlib:armhf (2.7.11-9) ...
Setting up python2.7 (2.7.11-9) ...
Setting up libpython-stdlib:armhf (2.7.11-1) ...
Setting up python (2.7.11-1) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
Setting up libnettle6:armhf (3.2-1) ...
Setting up libhogweed4:armhf (3.2-1) ...
Setting up libidn11:armhf (1.32-3) ...
Setting up libp11-kit0:armhf (0.23.2-3) ...
Setting up libtasn1-6:armhf (4.8-1) ...
Setting up libgnutls30:armhf (3.4.12-1) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up libkrb5support0:armhf (1.13.2+dfsg-5) ...
Setting up libk5crypto3:armhf (1.13.2+dfsg-5) ...
Setting up libkrb5-3:armhf (1.13.2+dfsg-5) ...
Setting up libgssapi-krb5-2:armhf (1.13.2+dfsg-5) ...
Setting up libsasl2-modules-db:armhf (2.1.26.dfsg1-15) ...
Setting up libsasl2-2:armhf (2.1.26.dfsg1-15) ...
Setting up libldap-2.4-2:armhf (2.4.42+dfsg-2+rpi1+b2) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up m4 (1.4.17-5) ...
Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20160430.1) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.19.7-2) ...
Setting up libglib2.0-0:armhf (2.48.1-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.57-1) ...
Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libtool (2.4.6-0.1) ...
Setting up libbambamc0 (0.0.50-1) ...
Setting up pkg-config (0.29-4) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libbambamc-dev (0.0.50-1) ...
Setting up libnghttp2-14:armhf (1.10.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up libssh2-1:armhf (1.5.0-2.1) ...
Setting up libcurl3-gnutls:armhf (7.47.0-1) ...
Setting up libhts1:armhf (1.3.1-1+rpi1) ...
Setting up samtools (1.3.1-2) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (9.20160403) ...
Setting up sbuild-build-depends-smalt-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Processing triggers for libc-bin (2.22-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.7 g++-5_5.3.1-19 gcc-5_5.3.1-19 libc6-dev_2.22-7 libstdc++-5-dev_5.3.1-19 libstdc++6_6.1.1-1+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.114 apt_1.2.12 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.28-5 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-19 dash_0.5.8-2.2 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160403 debianutils_4.7 dh-autoreconf_12 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.124-1 dpkg_1.18.7 dpkg-dev_1.18.7 e2fslibs_1.43~WIP.2016.03.15-2 e2fsprogs_1.43~WIP.2016.03.15-2 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-19 gcc_4:5.3.1-1+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_4.9.3-14 gcc-5_5.3.1-19 gcc-5-base_5.3.1-19 gcc-6-base_6.1.1-1+rpi1 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-6 gpgv_1.4.20-6 grep_2.25-1 groff-base_1.22.3-7 gzip_1.6-5 hostname_3.17 init_1.33 init-system-helpers_1.33 initscripts_2.88dsf-59.4 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-8+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10-4 libapt-pkg5.0_1.2.12 libarchive-zip-perl_1.57-1 libasan2_5.3.1-19 libatomic1_6.1.1-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.5.2-1+rpi1 libaudit1_1:2.5.2-1+rpi1 libbambamc-dev_0.0.50-1 libbambamc0_0.0.50-1 libblkid1_2.28-5 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-7 libc-dev-bin_2.22-7 libc6_2.22-7 libc6-dev_2.22-7 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_6.1.1-1+rpi1 libcomerr2_1.43~WIP.2016.03.15-2 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libcurl3-gnutls_7.47.0-1 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.210 libdevmapper1.02.1_2:1.02.124-1 libdpkg-perl_1.18.7 libdrm2_2.4.68-1 libexpat1_2.1.1-2 libfakeroot_1.20.2-1 libfdisk1_2.28-5 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgc1c2_1:7.4.2-7.4 libgcc-5-dev_5.3.1-19 libgcc1_1:6.1.1-1+rpi1 libgcrypt20_1.7.0-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.48.1-1 libgmp10_2:6.1.0+dfsg-2 libgnutls30_3.4.12-1 libgomp1_6.1.1-1+rpi1 libgpg-error0_1.22-2 libgssapi-krb5-2_1.13.2+dfsg-5 libhogweed4_3.2-1 libhts1_1.3.1-1+rpi1 libicu55_55.1-7 libidn11_1.32-3 libisl15_0.16.1-1 libk5crypto3_1.13.2+dfsg-5 libkeyutils1_1.5.9-9 libklibc_2.0.4-8+rpi1 libkmod2_22-1.1 libkrb5-3_1.13.2+dfsg-5 libkrb5support0_1.13.2+dfsg-5 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b2 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.28-5 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160319-1 libncursesw5_6.0+20160319-1 libnettle6_3.2-1 libnghttp2-14_1.10.0-1 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-3.1 libperl5.22_5.22.2-1 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps5_2:3.3.11-3 libpython-stdlib_2.7.11-1 libpython2.7-minimal_2.7.11-9 libpython2.7-stdlib_2.7.11-9 libreadline6_6.3-8+b3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.0-1 libselinux1_2.5-2 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28-5 libsqlite3-0_3.12.2-1 libss2_1.43~WIP.2016.03.15-2 libssh2-1_1.5.0-2.1 libssl1.0.2_1.0.2h-1 libstdc++-5-dev_5.3.1-19 libstdc++6_6.1.1-1+rpi1 libsystemd0_229-5 libtasn1-6_4.8-1 libtext-charwidth-perl_0.04-7+b6 libtext-iconv-perl_1.7-5+b7 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160319-1 libtool_2.4.6-0.1 libubsan0_6.1.1-1+rpi1 libudev1_229-5 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28-5 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.06-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28-5 multiarch-support_2.22-7 nano_2.5.3-3 ncurses-base_6.0+20160319-1 ncurses-bin_6.0+20160319-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.2-1 perl-base_5.22.2-1 perl-modules-5.22_5.22.2-1 pkg-config_0.29-4 po-debconf_1.0.19 procps_2:3.3.11-3 python_2.7.11-1 python-minimal_2.7.11-1 python2.7_2.7.11-9 python2.7-minimal_2.7.11-9 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 samtools_1.3.1-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-smalt-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_229-5 systemd-sysv_229-5 sysv-rc_2.88dsf-59.4 sysvinit-utils_2.88dsf-59.4 tar_1.28-2.2+rpi1 tzdata_2016d-2 udev_229-5 util-linux_2.28-5 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon May 23 10:21:17 2016 UTC using RSA key ID F09F4872
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./smalt_0.7.6-6.dsc
dpkg-source: info: extracting smalt in smalt-0.7.6
dpkg-source: info: unpacking smalt_0.7.6.orig.tar.gz
dpkg-source: info: unpacking smalt_0.7.6-6.debian.tar.xz
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-8901f23e-1caf-4a7f-8f25-34cb8189a0d4
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package smalt
dpkg-buildpackage: info: source version 0.7.6-6
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 --with autotools_dev # this fails because auf broken upstream autoconf stuff: - - with autoreconf
dh_testdir
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_autotools-dev_restoreconfig
dh_clean
debian/rules build-arch
dh build-arch --with autotools_dev # this fails because auf broken upstream autoconf stuff: - - with autoreconf
dh_testdir -a
dh_update_autotools_config -a
dh_autotools-dev_updateconfig -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 -fPIE -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 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -MT sequence.o -MD -MP -MF .deps/sequence.Tpo -c -o sequence.o sequence.c
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 -fPIE -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
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 -fPIE -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 -fPIE -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 -fPIE -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 -fPIE -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 -fPIE -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 -fPIE -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 -fPIE -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)
^
hashidx.c: 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)
^
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 -fPIE -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 -fPIE -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:1330:13: warning: 'labelSEGCANDWithinInsertRange' defined but not used [-Wunused-function]
static void labelSEGCANDWithinInsertRange (SEGCAND *candAp, SEGNUM_t nsegA,
^
segment.c:1375:12: warning: 'checkCANDARRsequential' defined but not used [-Wunused-function]
static int checkCANDARRsequential(const CANDARR candr, SEGNUM_t *rvc_offs)
^
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 -fPIE -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 -fPIE -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 -fPIE -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 -fPIE -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 -fPIE -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-results.Tpo .deps/smalt-results.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fPIE -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 -fPIE -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 -fPIE -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 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 -fPIE -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 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 -fPIE -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 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 -fPIE -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 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 -fPIE -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 -fPIE -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 -fPIE -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 -fPIE -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 -fPIE -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-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 -fPIE -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 -fPIE -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 -fPIE -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 -fPIE -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 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -fPIE -pie -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 --with autotools_dev # 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_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-6_armhf.deb'.
dpkg-deb: building package 'smalt' in '../smalt_0.7.6-6_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../smalt_0.7.6-6_armhf.changes
dpkg-genchanges: warning: package smalt-dbgsym listed in files list but not in control info
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 20160529-1222
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
smalt_0.7.6-6_armhf.changes:
----------------------------
Format: 1.8
Date: Mon, 23 May 2016 09:58:22 +0000
Source: smalt
Binary: smalt smalt-examples
Architecture: armhf
Version: 0.7.6-6
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <sascha@steinbiss.name>
Description:
smalt - Sequence Mapping and Alignment Tool
smalt-examples - Sequence Mapping and Alignment Tool (examples)
Changes:
smalt (0.7.6-6) unstable; urgency=medium
.
* Team upload.
* Remove Makefile from installed test data.
This differs in cross-arch builds, breaking i386 reproducibility
(and serves no purpose anyway).
Checksums-Sha1:
7b69144326c88ae4b988cebe4903904c92c2c373 294756 smalt-dbgsym_0.7.6-6_armhf.deb
3da705a811bebffd75a6b3fb7e02ff3080ae696e 96568 smalt_0.7.6-6_armhf.deb
Checksums-Sha256:
d006a5b7af36d36740a7b6acff1460afe5200c1b2a6af37bf6cf099025b98053 294756 smalt-dbgsym_0.7.6-6_armhf.deb
e9968f8f1be2263d92befd55be0a2e8d18277a38781a35f068bbc9a640f78472 96568 smalt_0.7.6-6_armhf.deb
Files:
e6cc2390a752b7ba4980c6eb3774171c 294756 debug extra smalt-dbgsym_0.7.6-6_armhf.deb
00842994fcc6371fdee62c7c8a850d3b 96568 science optional smalt_0.7.6-6_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
smalt-dbgsym_0.7.6-6_armhf.deb
------------------------------
new debian package, version 2.0.
size 294756 bytes: control archive=556 bytes.
456 bytes, 13 lines control
212 bytes, 2 lines md5sums
Package: smalt-dbgsym
Source: smalt
Version: 0.7.6-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 335
Depends: smalt (= 0.7.6-6)
Section: debug
Priority: extra
Homepage: http://www.sanger.ac.uk/science/tools/smalt-0
Description: Debug symbols for smalt
Auto-Built-Package: debug-symbols
Build-Ids: 12e657a89846e4e7b56d71c7c5771fe422576cc7 d394bffa34e796ab50f3c3f76f581baf3e8f91ad
drwxr-xr-x root/root 0 2016-05-29 12:22 ./
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/lib/
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/lib/debug/.build-id/12/
-rw-r--r-- root/root 276592 2016-05-29 12:22 ./usr/lib/debug/.build-id/12/e657a89846e4e7b56d71c7c5771fe422576cc7.debug
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/lib/debug/.build-id/d3/
-rw-r--r-- root/root 54204 2016-05-29 12:22 ./usr/lib/debug/.build-id/d3/94bffa34e796ab50f3c3f76f581baf3e8f91ad.debug
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/share/
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-05-29 12:22 ./usr/share/doc/smalt-dbgsym -> smalt
smalt_0.7.6-6_armhf.deb
-----------------------
new debian package, version 2.0.
size 96568 bytes: control archive=1131 bytes.
1293 bytes, 30 lines control
334 bytes, 5 lines md5sums
Package: smalt
Version: 0.7.6-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 256
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 2016-05-29 12:22 ./
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/bin/
-rwxr-xr-x root/root 202240 2016-05-29 12:22 ./usr/bin/smalt
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/lib/
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/lib/smalt/
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/lib/smalt/test/
-rwxr-xr-x root/root 42444 2016-05-29 12:22 ./usr/lib/smalt/test/sequenceReverseComplement_test
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/share/
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/share/doc/smalt/
-rw-r--r-- root/root 759 2016-05-23 10:16 ./usr/share/doc/smalt/changelog.Debian.gz
-rw-r--r-- root/root 1182 2015-04-14 06:44 ./usr/share/doc/smalt/copyright
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/share/man/
drwxr-xr-x root/root 0 2016-05-29 12:22 ./usr/share/man/man1/
-rw-r--r-- root/root 884 2016-05-29 12:22 ./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: 80756
Build-Time: 1944
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 361
Job: smalt_0.7.6-6
Machine Architecture: armhf
Package: smalt
Package-Time: 2387
Source-Version: 0.7.6-6
Space: 80756
Status: successful
Version: 0.7.6-6
--------------------------------------------------------------------------------
Finished at 20160529-1222
Build needed 00:39:47, 80756k disc space