[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_arm64_6 #1796

Sat Jan 14 17:10:28 UTC 2017

https://jenkins.debian.net/job/reproducible_builder_arm64_6/1796/------------------------------------------
[...truncated 18.59 KB...]
I: unmounting run/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/11207 and its subdirectories
+ PRESULT=1
+ '[' 1 -eq 124 ']'
+ false
+ set +x
Sat Jan 14 17:10:25 UTC 2017  I: Signing ./b1/ariba_2.6.1+ds-1_arm64.buildinfo as ariba_2.6.1+ds-1_arm64.buildinfo.asc
gpg: can't open `./b1/ariba_2.6.1+ds-1_arm64.buildinfo': No such file or directory
gpg: ./b1/ariba_2.6.1+ds-1_arm64.buildinfo: clearsign failed: file open error
Sat Jan 14 17:10:25 UTC 2017  E: Could not sign /srv/reproducible-results/rbuild-debian-IqIOF7G8/./b1/ariba_2.6.1+ds-1_arm64.buildinfo
Sat Jan 14 17:10:25 UTC 2017  I: Signed ./b1/ariba_2.6.1+ds-1_arm64.buildinfo as ./b1/ariba_2.6.1+ds-1_arm64.buildinfo.asc
Sat Jan 14 17:10:25 UTC 2017 - build #1 for ariba/unstable/arm64 on codethink-sled14-arm64 done.
Starting cleanup.
/srv/reproducible-results/rbuild-debian-kXtqqjuz/tmp.dzxH9FQxcO:	 73.3% -- replaced with /srv/reproducible-results/rbuild-debian-kXtqqjuz/tmp.dzxH9FQxcO.gz
All cleanup done.
Sat Jan 14 17:10:25 UTC 2017 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-6RMyFyeh, which will now be removed.
/srv/reproducible-results/rbuild-debian-IqIOF7G8:
total 16
-rw-r--r-- 1 jenkins jenkins 2209 Dec 21 20:28 ariba_2.6.1+ds-1.dsc
drwxr-xr-x 2 jenkins jenkins 4096 Jan 14 17:10 b1
drwxr-xr-x 2 jenkins jenkins 4096 Jan 14 17:10 b2
-rw------- 1 jenkins jenkins 3350 Jan 14 17:10 tmp.GXr9i4RFPd

/srv/reproducible-results/rbuild-debian-IqIOF7G8/b1:
total 12
-rw-r--r-- 1 jenkins jenkins 9595 Jan 14 17:10 build.log

/srv/reproducible-results/rbuild-debian-IqIOF7G8/b2:
total 0
I: using fakeroot in build.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Jan 14 05:10:06 -12 2017
I: pbuilder-time-stamp: 1484413806
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
I: mounting /proc filesystem
I: mounting /sys filesystem
I: mounting /run/shm filesystem
I: mounting /dev/pts filesystem
I: Mounting /dev/shm
I: policy-rc.d already exists
I: Copying source file
I: copying [ariba_2.6.1+ds-1.dsc]
I: copying [./ariba_2.6.1+ds.orig.tar.xz]
I: copying [./ariba_2.6.1+ds-1.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Dec 21 08:16:44 2016 -12
gpgv:                using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./ariba_2.6.1+ds-1.dsc
dpkg-source: info: extracting ariba in ariba-2.6.1+ds
dpkg-source: info: unpacking ariba_2.6.1+ds.orig.tar.xz
dpkg-source: info: unpacking ariba_2.6.1+ds-1.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_libs_for_extension.patch
I: Installing the build-deps
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <pbuilder-maint at lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper (>= 9), python3, python3-dev, python3-dendropy (>= 4.1.0), python3-setuptools, python3-pymummer (>= 0.10.1), python3-pysam (>= 0.9.1), python3-nose (>= 1.3), bowtie2 (>= 2.1.0), cd-hit, mash, libminimap-dev, libfml-dev, mummer, fastaq (>= 3.12.0), help2man, asciidoctor
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 18464 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper (>= 9); however:
  Package debhelper is not installed.
 pbuilder-satisfydepends-dummy depends on python3; however:
  Package python3 is not installed.
 pbuilder-satisfydepends-dummy depends on python3-dev; however:
  Package python3-dev is not installed.
 pbuilder-satisfydepends-dummy depends on python3-dendropy (>= 4.1.0); however:
  Package python3-dendropy is not installed.
 pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
  Package python3-setuptools is not installed.
 pbuilder-satisfydepends-dummy depends on python3-pymummer (>= 0.10.1); however:
  Package python3-pymummer is not installed.
 pbuilder-satisfydepends-dummy depends on python3-pysam (>= 0.9.1); however:
  Package python3-pysam is not installed.
 pbuilder-satisfydepends-dummy depends on python3-nose (>= 1.3); however:
  Package python3-nose is not installed.
 pbuilder-satisfydepends-dummy depends on bowtie2 (>= 2.1.0); however:
  Package bowtie2 is not installed.
 pbuilder-satisfydepends-dummy depends on cd-hit; however:
  Package cd-hit is not installed.
 pbuilder-satisfydepends-dummy depends on mash; however:
  Package mash is not installed.
 pbuilder-satisfydepends-dummy depends on libminimap-dev; however:
  Package libminimap-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libfml-dev; however:
  Package libfml-dev is not installed.
 pbuilder-satisfydepends-dummy depends on mummer; however:
  Package mummer is not installed.
 pbuilder-satisfydepends-dummy depends on fastaq (>= 3.12.0); however:
  Package fastaq is not installed.
 pbuilder-satisfydepends-dummy depends on help2man; however:
  Package help2man is not installed.
 pbuilder-satisfydepends-dummy depends on asciidoctor; however:
  Package asciidoctor is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} ca-certificates{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} fastaq{a} file{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcapnp-0.5.3{a} libcroco3{a} libcurl3-gnutls{a} libexpat1{a} libexpat1-dev{a} libffi6{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgnutls30{a} libgsl2{a} libgssapi-krb5-2{a} libhogweed4{a} libhts1{a} libicu57{a} libidn11{a} libidn2-0{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libminimap-dev{a} libminimap0{a} libmpdec2{a} libnettle6{a} libnghttp2-14{a} libp11-kit0{a} libpipeline1{a} libpsl5{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.5{a} libpython3.5-dev{a} libpython3.5-minimal{a} libpython3.5-stdlib{a} librtmp1{a} libruby2.3{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.0.2{a} libssl1.1{a} libtasn1-6{a} libtimedate-perl{a} libtool{a} libunistring0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} mash{a} mime-support{a} mummer{a} openssl{a} po-debconf{a} python3{a} python3-dendropy{a} python3-dev{a} python3-minimal{a} python3-nose{a} python3-pkg-resources{a} python3-pymummer{a} python3-pysam{a} python3-setuptools{a} python3.5{a} python3.5-dev{a} python3.5-minimal{a} rake{a} ruby{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-test-unit{a} ruby2.3{a} rubygems-integration{a} samtools{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  curl fonts-lato krb5-locales libglib2.0-data libjs-jquery libltdl-dev libmail-sendmail-perl libsasl2-modules lynx-cur publicsuffix python shared-mime-info wget xdg-user-dirs xml-core zip 
0 packages upgraded, 105 newly installed, 0 to remove and 0 not upgraded.
Need to get 49.9 MB of archives. After unpacking 230 MB will be used.
The following packages have unmet dependencies:
 pbuilder-satisfydepends-dummy : Depends: bowtie2 (>= 2.1.0) which is a virtual package and is not provided by any available package

                                 Depends: libfml-dev which is a virtual package and is not provided by any available package

Unable to resolve dependencies!  Giving up...
The following NEW packages will be installed:
  asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} ca-certificates{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} fastaq{a} file{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcapnp-0.5.3{a} libcroco3{a} libcurl3-gnutls{a} libexpat1{a} libexpat1-dev{a} libffi6{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgnutls30{a} libgsl2{a} libgssapi-krb5-2{a} libhogweed4{a} libhts1{a} libicu57{a} libidn11{a} libidn2-0{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libminimap-dev{a} libminimap0{a} libmpdec2{a} libnettle6{a} libnghttp2-14{a} libp11-kit0{a} libpipeline1{a} libpsl5{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.5{a} libpython3.5-dev{a} libpython3.5-minimal{a} libpython3.5-stdlib{a} librtmp1{a} libruby2.3{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.0.2{a} libssl1.1{a} libtasn1-6{a} libtimedate-perl{a} libtool{a} libunistring0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} mash{a} mime-support{a} mummer{a} openssl{a} po-debconf{a} python3{a} python3-dendropy{a} python3-dev{a} python3-minimal{a} python3-nose{a} python3-pkg-resources{a} python3-pymummer{a} python3-pysam{a} python3-setuptools{a} python3.5{a} python3.5-dev{a} python3.5-minimal{a} rake{a} ruby{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-test-unit{a} ruby2.3{a} rubygems-integration{a} samtools{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  curl fonts-lato krb5-locales libglib2.0-data libjs-jquery libltdl-dev libmail-sendmail-perl libsasl2-modules lynx-cur publicsuffix python shared-mime-info wget xdg-user-dirs xml-core zip 
0 packages upgraded, 105 newly installed, 0 to remove and 0 not upgraded.
Need to get 49.9 MB of archives. After unpacking 230 MB will be used.
Abort.
E: pbuilder-satisfydepends failed.
I: unmounting /dev/shm filesystem
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/11207 and its subdirectories
removed ‘/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/ariba_2.6.1+ds-1.rbuild.log.gz’
removed ‘/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/ariba_2.6.1+ds-1.build1.log.gz’
+ echo 'Compressing the 1st log...'
Compressing the 1st log...
+ gzip -9cvn b1/build.log
b1/build.log:	 74.4%
+ chmod 644 /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/ariba_2.6.1+ds-1.build1.log.gz
+ update_rbuildlog
+ chmod 644 /srv/reproducible-results/rbuild-debian-IqIOF7G8/tmp.GXr9i4RFPd
+ mv /srv/reproducible-results/rbuild-debian-IqIOF7G8/tmp.GXr9i4RFPd /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/ariba_2.6.1+ds-1.rbuild.log
+ RBUILDLOG=/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/ariba_2.6.1+ds-1.rbuild.log
+ '[' 1 -eq 1 ']'
+ handle_ftbfs
+ false
+ set +x
ariba failed to build from source.
E: pbuilder-satisfydepends failed.
Sat Jan 14 17:10:27 UTC 2017  W: Downloading the build dependencies failed
Sat Jan 14 17:10:27 UTC 2017  W: Maybe there was a network problem, or the build dependencies are currently uninstallable; consider filing a bug in the last case.
Sat Jan 14 17:10:27 UTC 2017  W: Network problems are automatically rescheduled after some hours.
psql: server closed the connection unexpectedly
	This probably means the server terminated abnormally
	before or while processing the request.
psql: could not connect to server: No such file or directory
	Is the server running locally and accepting
	connections on Unix domain socket "/var/run/postgresql/.s.PGSQL.5432"?
psql: could not connect to server: No such file or directory
	Is the server running locally and accepting
	connections on Unix domain socket "/var/run/postgresql/.s.PGSQL.5432"?
Starting cleanup.
/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/ariba_2.6.1+ds-1.rbuild.log:	 68.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/ariba_2.6.1+ds-1.rbuild.log.gz
INFO: Starting at 2017-01-14 17:10:27.916080
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/sqlalchemy/pool.py", line 950, in _do_get
    return self._pool.get(wait, self._timeout)
  File "/usr/lib/python3/dist-packages/sqlalchemy/util/queue.py", line 145, in get
    raise Empty
sqlalchemy.util.queue.Empty

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/sqlalchemy/engine/strategies.py", line 90, in connect
    return dialect.connect(*cargs, **cparams)
  File "/usr/lib/python3/dist-packages/sqlalchemy/engine/default.py", line 377, in connect
    return self.dbapi.connect(*cargs, **cparams)
  File "/usr/lib/python3/dist-packages/psycopg2/__init__.py", line 164, in connect
    conn = _connect(dsn, connection_factory=connection_factory, async=async)
psycopg2.OperationalError: could not connect to server: No such file or directory
	Is the server running locally and accepting
	connections on Unix domain socket "/var/run/postgresql/.s.PGSQL.5432"?

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/srv/jenkins/bin/reproducible_html_packages.py", line 13, in <module>
    from reproducible_common import *
  File "/srv/jenkins/bin/reproducible_common.py", line 126, in <module>
    conn_db = DB_ENGINE.connect()      # the local postgres reproducible db
  File "/usr/lib/python3/dist-packages/sqlalchemy/engine/base.py", line 1778, in connect
    return self._connection_cls(self, **kwargs)
  File "/usr/lib/python3/dist-packages/sqlalchemy/engine/base.py", line 60, in __init__
    self.__connection = connection or engine.raw_connection()
  File "/usr/lib/python3/dist-packages/sqlalchemy/engine/base.py", line 1847, in raw_connection
    return self.pool.unique_connection()
  File "/usr/lib/python3/dist-packages/sqlalchemy/pool.py", line 280, in unique_connection
    return _ConnectionFairy._checkout(self)
  File "/usr/lib/python3/dist-packages/sqlalchemy/pool.py", line 644, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
  File "/usr/lib/python3/dist-packages/sqlalchemy/pool.py", line 440, in checkout
    rec = pool._do_get()
  File "/usr/lib/python3/dist-packages/sqlalchemy/pool.py", line 963, in _do_get
    return self._create_connection()
  File "/usr/lib/python3/dist-packages/sqlalchemy/pool.py", line 285, in _create_connection
    return _ConnectionRecord(self)
  File "/usr/lib/python3/dist-packages/sqlalchemy/pool.py", line 411, in __init__
    self.connection = self.__connect()
  File "/usr/lib/python3/dist-packages/sqlalchemy/pool.py", line 538, in __connect
    connection = self.__pool._creator()
  File "/usr/lib/python3/dist-packages/sqlalchemy/engine/strategies.py", line 96, in connect
    connection_invalidated=invalidated
  File "/usr/lib/python3/dist-packages/sqlalchemy/util/compat.py", line 188, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb, cause=exc_value)
  File "/usr/lib/python3/dist-packages/sqlalchemy/util/compat.py", line 181, in reraise
    raise value.with_traceback(tb)
  File "/usr/lib/python3/dist-packages/sqlalchemy/engine/strategies.py", line 90, in connect
    return dialect.connect(*cargs, **cparams)
  File "/usr/lib/python3/dist-packages/sqlalchemy/engine/default.py", line 377, in connect
    return self.dbapi.connect(*cargs, **cparams)
  File "/usr/lib/python3/dist-packages/psycopg2/__init__.py", line 164, in connect
    conn = _connect(dsn, connection_factory=connection_factory, async=async)
sqlalchemy.exc.OperationalError: (OperationalError) could not connect to server: No such file or directory
	Is the server running locally and accepting
	connections on Unix domain socket "/var/run/postgresql/.s.PGSQL.5432"?
 None None
Warning: cannot update HTML pages for ariba
All cleanup done.
Sat 14 Jan 17:10:28 UTC 2017 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-XsS91SmW, which will now be removed.
Build step 'Execute shell' marked build as failure