=> Building biology/bowtie2 build started at Wed Oct 5 13:44:03 PDT 2016 port directory: /usr/ports/biology/bowtie2 building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.78.g7d868-DEVELOPMENT #7: Mon Aug 1 22:25:32 PDT 2016 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: bacon4000@gmail.com ident warning: no id keywords in /build/boomdata/data/.m/bleeding-edge-default/ref/../09//usr/ports/biology/bowtie2/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400702 !!! Jail is newer than host. (Jail: 400702, Host: 400700) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/bleeding-edge-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=bowtie2-2.2.8 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/bleeding-edge-default/ref/.p/pool MASTERNAME=bleeding-edge-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---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/biology/bowtie2 XDG_CONFIG_HOME=/wrkdirs/biology/bowtie2 HOME=/wrkdirs/biology/bowtie2 TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/bowtie2 XDG_CONFIG_HOME=/wrkdirs/biology/bowtie2 HOME=/wrkdirs/biology/bowtie2 TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -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=4.7 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 PROFILE="@comment " DOCSDIR="share/doc/bowtie2" EXAMPLESDIR="share/examples/bowtie2" DATADIR="share/bowtie2" WWWDIR="www/bowtie2" ETCDIR="etc/bowtie2" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bowtie2 DOCSDIR=/usr/local/share/doc/bowtie2 EXAMPLESDIR=/usr/local/share/examples/bowtie2 WWWDIR=/usr/local/www/bowtie2 ETCDIR=/usr/local/etc/bowtie2 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> bowtie2-2.2.8 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz Installing pkg-1.8.7_3... Extracting pkg-1.8.7_3: .......... done ===> bowtie2-2.2.8 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bowtie2-2.2.8 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bowtie2-2.2.8 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bowtie2-2.2.8 for building => SHA256 Checksum OK for BenLangmead-bowtie2-v2.2.8_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by bowtie2-2.2.8 for building ===> Extracting for bowtie2-2.2.8 => SHA256 Checksum OK for BenLangmead-bowtie2-v2.2.8_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for bowtie2-2.2.8 ===> Applying ports patches for bowtie2-2.2.8 =========================================================================== =================================================== ===> bowtie2-2.2.8 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz Installing gmake-4.2.1_1... `-- Installing indexinfo-0.2.5... `-- Extracting indexinfo-0.2.5: .... done `-- Installing gettext-runtime-0.19.8.1... `-- Extracting gettext-runtime-0.19.8.1: .......... done Extracting gmake-4.2.1_1: .......... done ===> bowtie2-2.2.8 depends on executable: gmake - found ===> Returning to build of bowtie2-2.2.8 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for bowtie2-2.2.8 =========================================================================== =================================================== ===> Building for bowtie2-2.2.8 gmake[1]: Entering directory '/wrkdirs/biology/bowtie2/bowtie2-2.2.8' c++ -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o bowtie2-build-s bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \ -lpthread c++ -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -o bowtie2-build-l bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \ -lpthread c++ -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o bowtie2-align-s bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -lpthread c++ -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -o bowtie2-align-l bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -lpthread c++ -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops \ -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \ -I third_party -I . \ -o bowtie2-inspect-s bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread c++ -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops \ -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -DBOWTIE_64BIT_INDEX -Wall \ -I third_party -I . \ -o bowtie2-inspect-l bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread In file included from aligner_seed2.cpp:22:0: aligner_seed2.h: In member function 'size_t Descent::recalcOutgoing(const Read&, const Scoring&, TAlScore, TAlScore, DescentRedundancyChecker&, EFactory&, const EList&, const EList&, PerReadMetrics&)': aligner_seed2.h:1019:13: warning: 'edge.DescentEdge::nex' may be used uninitialized in this function [-Wmaybe-uninitialized] best1 = e; ^ aligner_seed2.cpp:585:14: note: 'edge.DescentEdge::nex' was declared here DescentEdge edge; ^ gmake[1]: Leaving directory '/wrkdirs/biology/bowtie2/bowtie2-2.2.8' =========================================================================== =================================================== ===> bowtie2-2.2.8 depends on package: perl5>=5.20<5.21 - not found ===> Installing existing package /packages/All/perl5-5.20.3_15.txz Installing perl5-5.20.3_15... Extracting perl5-5.20.3_15: .......... done Message from perl5-5.20.3_15: 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. ===> bowtie2-2.2.8 depends on package: perl5>=5.20<5.21 - found ===> Returning to build of bowtie2-2.2.8 =========================================================================== =================================================== ===> Staging for bowtie2-2.2.8 ===> Generating temporary packing list gmake[1]: Entering directory '/wrkdirs/biology/bowtie2/bowtie2-2.2.8' mkdir -p /wrkdirs/biology/bowtie2/stage/usr/local/bin for file in bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-inspect bowtie2-build bowtie2 ; do \ cp -f $file /wrkdirs/biology/bowtie2/stage/usr/local/bin ; \ done gmake[1]: Leaving directory '/wrkdirs/biology/bowtie2/bowtie2-2.2.8' /bin/mkdir -p /wrkdirs/biology/bowtie2/stage/usr/local/share/bowtie2/scripts install -s -m 555 /wrkdirs/biology/bowtie2/bowtie2-2.2.8/bowtie2*-s /wrkdirs/biology/bowtie2/bowtie2-2.2.8/bowtie2*-l /wrkdirs/biology/bowtie2/stage/usr/local/bin install -m 555 /wrkdirs/biology/bowtie2/bowtie2-2.2.8/scripts/*.sh /wrkdirs/biology/bowtie2/bowtie2-2.2.8/scripts/*.pl /wrkdirs/biology/bowtie2/stage/usr/local/share/bowtie2/scripts cd /wrkdirs/biology/bowtie2/bowtie2-2.2.8/example && /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/{} \;' -- 'index reads reference' /wrkdirs/biology/bowtie2/stage/usr/local/share/examples/bowtie2 cd /wrkdirs/biology/bowtie2/bowtie2-2.2.8/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/biology/bowtie2/stage/usr/local/share/doc/bowtie2 ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for bowtie2-2.2.8 file sizes/checksums [67]: . done packing files [67]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for bowtie2-2.2.8 build of biology/bowtie2 ended at Wed Oct 5 13:48:01 PDT 2016 build time: 00:03:58