Attachment 166590 Details for Bug 206939 – Poudriere log

Poudriere log

bowtie-1.1.2.log-9-3-amd64 (text/plain), 17.90 KB, created by Jason W. Bacon on 2016-02-05 03:53:09 UTC

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Creator: Jason W. Bacon

Created: 2016-02-05 03:53:09 UTC

Size: 17.90 KB

patch

obsolete

>build started at Thu Feb  4 21:47:53 CST 2016
>port directory: /usr/ports/biology/bowtie
>building for: FreeBSD 9-3-amd64-default 9.3-RELEASE-p36 FreeBSD 9.3-RELEASE-p36 amd64
>maintained by: bacon4000@gmail.com
>ident warning: no id keywords in /usr/local/poudriere/data/.m/9-3-amd64-default/ref//usr/ports/biology/bowtie/Makefile
>Makefile ident: 
>Poudriere version: 3.1.10
>Host OSVERSION: 1001000
>Jail OSVERSION: 903000
>
>---Begin Environment---
>PKGREPOSITORY=/tmp/pkgs
>PACKAGES=/tmp/pkgs
>OSVERSION=903000
>UNAME_v=FreeBSD 9.3-RELEASE-p36
>UNAME_r=9.3-RELEASE-p36
>BLOCKSIZE=K
>MAIL=/var/mail/root
>STATUS=1
>WARNING_WAIT=0
>SAVED_TERM=xterm
>NO_WARNING_PKG_INSTALL_EOL=yes
>MASTERMNT=/usr/local/poudriere/data/.m/9-3-amd64-default/ref
>FORCE_PACKAGE=yes
>PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
>POUDRIERE_BUILD_TYPE=bulk
>OLDPWD=/usr/wip/biology/bowtie
>PWD=/
>MASTERNAME=9-3-amd64-default
>SCRIPTPREFIX=/usr/local/share/poudriere
>USER=root
>HOME=/root
>POUDRIERE_VERSION=3.1.10
>SCRIPTPATH=/usr/local/share/poudriere/testport.sh
>TRYBROKEN=yes
>LIBEXECPREFIX=/usr/local/libexec/poudriere
>LOCALBASE=/usr/local
>PACKAGE_BUILDING=yes
>DEV_WARNING_WAIT=0
>---End Environment---
>
>---Begin OPTIONS List---
>---End OPTIONS List---
>
>--CONFIGURE_ARGS--
>
>--End CONFIGURE_ARGS--
>
>--CONFIGURE_ENV--
>MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bowtie/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bowtie/work  HOME=/wrkdirs/usr/ports/biology/bowtie/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh
>--End CONFIGURE_ENV--
>
>--MAKE_ENV--
>XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bowtie/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bowtie/work  HOME=/wrkdirs/usr/ports/biology/bowtie/work TMPDIR="/tmp" DONTSTRIP=yes NO_PIE=yes NO_DEBUG_FILES=yes SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local  LOCALBASE=/usr/local  LIBDIR="/usr/lib"  CC="gcc" CFLAGS="-pipe -g -fstack-protector -fno-strict-aliasing"  CPP="gcpp" CPPFLAGS=""  LDFLAGS=" -fstack-protector" LIBS=""  CXX="g++" CXXFLAGS="-pipe -g -fstack-protector -fno-strict-aliasing"  MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install   -m 555"  BSD_INSTALL_LIB="install   -m 444"  BSD_INSTALL_SCRIPT="install  -m 555"  BSD_INSTALL_DATA="install  -m 0644"  BSD_INSTALL_MAN="install  -m 444"
>--End MAKE_ENV--
>
>--PLIST_SUB--
>OSREL=9.3
>PREFIX=%D
>LOCALBASE=/usr/local
>RESETPREFIX=/usr/local
>PORTDOCS=""
>PORTEXAMPLES=""
>LIB32DIR=lib
>PERL_VERSION=5.20.3
>PERL_VER=5.20
>PERL5_MAN1=lib/perl5/site_perl/man/man1
>PERL5_MAN3=lib/perl5/site_perl/man/man3
>SITE_PERL=lib/perl5/site_perl
>SITE_ARCH=lib/perl5/site_perl/mach/5.20
>DOCSDIR="share/doc/bowtie"
>EXAMPLESDIR="share/examples/bowtie"
>DATADIR="share/bowtie"
>WWWDIR="www/bowtie"
>ETCDIR="etc/bowtie"
>--End PLIST_SUB--
>
>--SUB_LIST--
>PREFIX=/usr/local
>LOCALBASE=/usr/local
>DATADIR=/usr/local/share/bowtie
>DOCSDIR=/usr/local/share/doc/bowtie
>EXAMPLESDIR=/usr/local/share/examples/bowtie
>WWWDIR=/usr/local/www/bowtie
>ETCDIR=/usr/local/etc/bowtie
>--End SUB_LIST--
>
>---Begin make.conf---
>USE_PACKAGE_DEPENDS=yes
>BATCH=yes
>WRKDIRPREFIX=/wrkdirs
>PORTSDIR=/usr/ports
>PACKAGES=/packages
>DISTDIR=/distfiles
>---End make.conf---
>=======================<phase: check-sanity   >============================
>===>  License ART10 accepted by the user
>===========================================================================
>=======================<phase: pkg-depends    >============================
>===>   bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - not found
>===>   Installing existing package /packages/All/pkg-1.6.3.txz
>[9-3-amd64-default] Installing pkg-1.6.3...
>[9-3-amd64-default] Extracting pkg-1.6.3: .......... done
>Message from pkg-1.6.3:
>If you are upgrading from the old package format, first run:
>
>  # pkg2ng
>===>   bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - found
>===>   Returning to build of bowtie-1.1.2
>===========================================================================
>=======================<phase: fetch-depends  >============================
>===========================================================================
>=======================<phase: fetch          >============================
>===>  License ART10 accepted by the user
>===>   bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by bowtie-1.1.2 for building
>===========================================================================
>=======================<phase: checksum       >============================
>===>  License ART10 accepted by the user
>===>   bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by bowtie-1.1.2 for building
>=> SHA256 Checksum OK for BenLangmead-bowtie-1.1.2-v1.1.2_GH0.tar.gz.
>===========================================================================
>=======================<phase: extract-depends>============================
>===========================================================================
>=======================<phase: extract        >============================
>===>  License ART10 accepted by the user
>===>   bowtie-1.1.2 depends on file: /usr/local/sbin/pkg - found
>===> Fetching all distfiles required by bowtie-1.1.2 for building
>===>  Extracting for bowtie-1.1.2
>=> SHA256 Checksum OK for BenLangmead-bowtie-1.1.2-v1.1.2_GH0.tar.gz.
>===========================================================================
>=======================<phase: patch-depends  >============================
>===========================================================================
>=======================<phase: patch          >============================
>===>  Patching for bowtie-1.1.2
>===>  Applying FreeBSD patches for bowtie-1.1.2
>===========================================================================
>=======================<phase: build-depends  >============================
>===>   bowtie-1.1.2 depends on executable: gmake - not found
>===>   Installing existing package /packages/All/gmake-4.1_2.txz
>[9-3-amd64-default] Installing gmake-4.1_2...
>[9-3-amd64-default] `-- Installing indexinfo-0.2.4...
>[9-3-amd64-default] `-- Extracting indexinfo-0.2.4: .... done
>[9-3-amd64-default] `-- Installing libiconv-1.14_9...
>[9-3-amd64-default] `-- Extracting libiconv-1.14_9: .......... done
>[9-3-amd64-default] `-- Installing gettext-runtime-0.19.6...
>[9-3-amd64-default] `-- Extracting gettext-runtime-0.19.6: .......... done
>[9-3-amd64-default] Extracting gmake-4.1_2: .......... done
>===>   bowtie-1.1.2 depends on executable: gmake - found
>===>   Returning to build of bowtie-1.1.2
>===========================================================================
>=======================<phase: lib-depends    >============================
>===========================================================================
>====>> Recording filesystem state for prebuild... done
>=======================<phase: configure      >============================
>===>   bowtie-1.1.2 depends on executable: gmake - found
>===>  Configuring for bowtie-1.1.2
>===========================================================================
>=======================<phase: build          >============================
>===>  Building for bowtie-1.1.2
>g++ -O -DCOMPILER_OPTIONS="\"-O  -DPOPCNT_CAPABILITY -pipe -g -fstack-protector -fno-strict-aliasing  -pipe -g -fstack-protector -fno-strict-aliasing \""  -DPOPCNT_CAPABILITY -pipe -g -fstack-protector -fno-strict-aliasing  -pipe -g -fstack-protector -fno-strict-aliasing   \
>	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
>	-I SeqAn-1.1 -I third_party -I third_party \
>	-o bowtie-build-s ebwt_build.cpp \
>	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
>	-lpthread 
>g++ -O -DCOMPILER_OPTIONS="\"-O  -DPOPCNT_CAPABILITY -pipe -g -fstack-protector -fno-strict-aliasing  -pipe -g -fstack-protector -fno-strict-aliasing \""  -DPOPCNT_CAPABILITY -pipe -g -fstack-protector -fno-strict-aliasing  -pipe -g -fstack-protector -fno-strict-aliasing   \
>	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
>	-I SeqAn-1.1 -I third_party -I third_party \
>	-o bowtie-build-l ebwt_build.cpp \
>	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
>	-lpthread 
>g++ -O -DCOMPILER_OPTIONS="\"-O  -DPOPCNT_CAPABILITY -pipe -g -fstack-protector -fno-strict-aliasing  -pipe -g -fstack-protector -fno-strict-aliasing \""  -DPOPCNT_CAPABILITY -pipe -g -fstack-protector -fno-strict-aliasing  -pipe -g -fstack-protector -fno-strict-aliasing  \
>	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
>	-I SeqAn-1.1 -I third_party -I third_party \
>	-o bowtie-align-s ebwt_search.cpp \
>	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
>	-lpthread 
>g++ -O -DCOMPILER_OPTIONS="\"-O  -DPOPCNT_CAPABILITY -pipe -g -fstack-protector -fno-strict-aliasing  -pipe -g -fstack-protector -fno-strict-aliasing \""  -DPOPCNT_CAPABILITY -pipe -g -fstack-protector -fno-strict-aliasing  -pipe -g -fstack-protector -fno-strict-aliasing  \
>	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -DBOWTIE_64BIT_INDEX -Wall \
>	-I SeqAn-1.1 -I third_party -I third_party \
>	-o bowtie-align-l ebwt_search.cpp \
>	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
>	-lpthread 
>g++ -O \
>	-DCOMPILER_OPTIONS="\"-O  -DPOPCNT_CAPABILITY -pipe -g -fstack-protector -fno-strict-aliasing  -pipe -g -fstack-protector -fno-strict-aliasing \""  -DPOPCNT_CAPABILITY -pipe -g -fstack-protector -fno-strict-aliasing  -pipe -g -fstack-protector -fno-strict-aliasing  \
>	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall \
>	-I SeqAn-1.1 -I third_party -I third_party -I . \
>	-o bowtie-inspect-s bowtie_inspect.cpp \
>	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp \
>	-lpthread
>g++ -O \
>	-DCOMPILER_OPTIONS="\"-O  -DPOPCNT_CAPABILITY -pipe -g -fstack-protector -fno-strict-aliasing  -pipe -g -fstack-protector -fno-strict-aliasing \""  -DPOPCNT_CAPABILITY -pipe -g -fstack-protector -fno-strict-aliasing  -pipe -g -fstack-protector -fno-strict-aliasing  \
>	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall \
>	-I SeqAn-1.1 -I third_party -I third_party -I . \
>	-o bowtie-inspect-l bowtie_inspect.cpp \
>	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp \
>	-lpthread
>===========================================================================
>====>> Checking for filesystem violations... done
>=======================<phase: run-depends    >============================
>===>   bowtie-1.1.2 depends on executable: webbrowser - not found
>===>   Installing existing package /packages/All/webbrowser-0.3.txz
>[9-3-amd64-default] Installing webbrowser-0.3...
>[9-3-amd64-default] Extracting webbrowser-0.3: ..... done
>===>   bowtie-1.1.2 depends on executable: webbrowser - found
>===>   Returning to build of bowtie-1.1.2
>===>   bowtie-1.1.2 depends on package: perl5>=5.20<5.21 - not found
>===>   Installing existing package /packages/All/perl5-5.20.3_8.txz
>[9-3-amd64-default] Installing perl5-5.20.3_8...
>[9-3-amd64-default] Extracting perl5-5.20.3_8: .......... done
>Message from perl5-5.20.3_8:
>The /usr/bin/perl symlink has been removed starting with Perl 5.20.
>For shebangs, you should either use:
>
>#!/usr/local/bin/perl
>
>or
>
>#!/usr/bin/env perl
>
>The first one will only work if you have a /usr/local/bin/perl,
>the second will work as long as perl is in PATH.
>===>   bowtie-1.1.2 depends on package: perl5>=5.20<5.21 - found
>===>   Returning to build of bowtie-1.1.2
>===========================================================================
>====>> Recording filesystem state for prestage... done
>=======================<phase: stage          >============================
>===>  Staging for bowtie-1.1.2
>===>   bowtie-1.1.2 depends on executable: webbrowser - found
>===>   bowtie-1.1.2 depends on package: perl5>=5.20<5.21 - found
>===>   Generating temporary packing list
>install  -m 555  /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/bowtie  /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/bowtie-build  /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/bowtie-inspect  /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/bin
>install   -m 555  /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/bowtie*-s  /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/bowtie*-l  /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/bin
>install  -m 555  /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/scripts/*.sh  /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/scripts/*.pl  /usr/ports/biology/bowtie/files/bowtie-manual  /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/bin
>/bin/mkdir -p /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/share/bowtie
>cd /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2 && /bin/sh -c '(/usr/bin/find -d $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null  2>&1) &&  /usr/bin/find -d $0 $2 -type d -exec chmod 755 $1/{} \; &&  /usr/bin/find -d $0 $2 -type f -exec chmod 444 $1/{} \;' --  'genomes indexes reads'  /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/share/bowtie
>cd /wrkdirs/usr/ports/biology/bowtie/work/bowtie-1.1.2/doc && /bin/sh -c '(/usr/bin/find -d $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null  2>&1) &&  /usr/bin/find -d $0 $2 -type d -exec chmod 755 $1/{} \; &&  /usr/bin/find -d $0 $2 -type f -exec chmod 444 $1/{} \;' --  \*  /wrkdirs/usr/ports/biology/bowtie/work/stage/usr/local/share/doc/bowtie
>====> Compressing man pages (compress-man)
>===========================================================================
>====> Running Q/A tests (stage-qa)
>====> Checking for pkg-plist issues (check-plist)
>===> Parsing plist
>===> Checking for items in STAGEDIR missing from pkg-plist
>===> Checking for items in pkg-plist which are not in STAGEDIR
>===> No pkg-plist issues found (check-plist)
>====>> Checking for staging violations... done
>=======================<phase: package        >============================
>===>  Building package for bowtie-1.1.2
>===========================================================================
>=======================<phase: install-mtree  >============================
>===========================================================================
>====>> Recording filesystem state for preinst... done
>=======================<phase: install        >============================
>===>  Installing for bowtie-1.1.2
>===>   bowtie-1.1.2 depends on executable: webbrowser - found
>===>   bowtie-1.1.2 depends on package: perl5>=5.20<5.21 - found
>===>  Checking if bowtie already installed
>===>   Registering installation for bowtie-1.1.2
>[9-3-amd64-default] Installing bowtie-1.1.2...
>===========================================================================
>====>> Checking shared library dependencies
> 0x0000000000000001 (NEEDED)             Shared library: [libc.so.7]
> 0x0000000000000001 (NEEDED)             Shared library: [libgcc_s.so.1]
> 0x0000000000000001 (NEEDED)             Shared library: [libm.so.5]
> 0x0000000000000001 (NEEDED)             Shared library: [libstdc++.so.6]
> 0x0000000000000001 (NEEDED)             Shared library: [libthr.so.3]
>=======================<phase: deinstall      >============================
>===>  Deinstalling for bowtie
>===>   Deinstalling bowtie-1.1.2
>Updating database digests format: ........ done
>Checking integrity... done (0 conflicting)
>Deinstallation has been requested for the following 1 packages (of 0 packages in the universe):
>
>Installed packages to be REMOVED:
>	bowtie-1.1.2
>
>The operation will free 27 MiB.
>[9-3-amd64-default] [1/1] Deinstalling bowtie-1.1.2...
>[9-3-amd64-default] [1/1] Deleting files for bowtie-1.1.2: .......... done
>===========================================================================
>====>> Checking for extra files and directories
>[00:01:06] ====>> Installing from package
>[9-3-amd64-default] Installing bowtie-1.1.2...
>[9-3-amd64-default] Extracting bowtie-1.1.2: .......... done
>[00:01:07] ====>> Cleaning up
>===>  Cleaning for bowtie-1.1.2
>[00:01:08] ====>> Deinstalling package
>Updating database digests format: . done
>Checking integrity... done (0 conflicting)
>Deinstallation has been requested for the following 1 packages (of 0 packages in the universe):
>
>Installed packages to be REMOVED:
>	bowtie-1.1.2
>
>The operation will free 27 MiB.
>[9-3-amd64-default] [1/1] Deinstalling bowtie-1.1.2...
>[9-3-amd64-default] [1/1] Deleting files for bowtie-1.1.2: .......... done
>build of biology/bowtie ended at Thu Feb  4 21:48:56 CST 2016
>build time: 00:01:03

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Attachments on bug 206939: 166589 | 166590 | 166591 | 167715 | 167716 | 167717