=> Building biology/bowtie2 Started : Wednesday, 18 APR 2018 at 02:02:45 UTC Platform: 5.3-DEVELOPMENT DragonFly v5.3.0.81.g32506c-DEVELOPMENT #29: Tue Apr 10 08:49:52 PDT 2018 marino@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.0-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.0-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for bowtie2-2.3.3.1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/construction/biology/bowtie2 XDG_CONFIG_HOME=/construction/biology/bowtie2 HOME=/construction/biology/bowtie2 TMPDIR="/tmp" PATH=/construction/biology/bowtie2/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/bowtie2 XDG_CONFIG_HOME=/construction/biology/bowtie2 HOME=/construction/biology/bowtie2 TMPDIR="/tmp" PATH=/construction/biology/bowtie2/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin 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 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/bowtie2/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly5 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=5.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.26.1 PERL_VER=5.26 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/5.26 PROFILE="@comment " DOCSDIR="share/doc/bowtie2" EXAMPLESDIR="share/examples/bowtie2" DATADIR="share/bowtie2" WWWDIR="www/bowtie2" ETCDIR="etc/bowtie2" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.0 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500000 OSVERSION=9999999 OSREL=5.0 _OSRELEASE=5.0-SYNTH -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3+ accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> bowtie2-2.3.3.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5.txz Installing pkg-1.10.5... Extracting pkg-1.10.5: .......... done ===> bowtie2-2.3.3.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bowtie2-2.3.3.1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by bowtie2-2.3.3.1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by bowtie2-2.3.3.1 for building => SHA256 Checksum OK for BenLangmead-bowtie2-v2.3.3.1_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by bowtie2-2.3.3.1 for building ===> Extracting for bowtie2-2.3.3.1 => SHA256 Checksum OK for BenLangmead-bowtie2-v2.3.3.1_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for bowtie2-2.3.3.1 ===> Applying ports patches for bowtie2-2.3.3.1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> bowtie2-2.3.3.1 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz Installing gmake-4.2.1_2... `-- Installing gettext-runtime-0.19.8.1_1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_1: .......... done Extracting gmake-4.2.1_2: .......... done ===> bowtie2-2.3.3.1 depends on executable: gmake - found ===> Returning to build of bowtie2-2.3.3.1 ===> bowtie2-2.3.3.1 depends on file: /usr/local/bin/python2.7 - not found ===> Installing existing package /packages/All/python27-2.7.14_1.txz Installing python27-2.7.14_1... `-- Installing expat-2.2.5... `-- Extracting expat-2.2.5: .......... done `-- Installing libffi-3.2.1_2... `-- Extracting libffi-3.2.1_2: .......... done `-- Installing libressl-2.6.4... `-- Extracting libressl-2.6.4: .......... done `-- Installing ncurses-6.0.0s20171223_1... `-- Extracting ncurses-6.0.0s20171223_1: .......... done `-- Installing readline-7.0.3_1... `-- Extracting readline-7.0.3_1: .......... done Extracting python27-2.7.14_1: .......... done Message from python27-2.7.14_1: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> bowtie2-2.3.3.1 depends on file: /usr/local/bin/python2.7 - found ===> Returning to build of bowtie2-2.3.3.1 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> bowtie2-2.3.3.1 depends on shared library: libtbb.so - not found ===> Installing existing package /packages/All/tbb-2018.2.txz Installing tbb-2018.2... Extracting tbb-2018.2: .......... done ===> bowtie2-2.3.3.1 depends on shared library: libtbb.so - found (/usr/local/lib/libtbb.so) ===> Returning to build of bowtie2-2.3.3.1 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for bowtie2-2.3.3.1 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for bowtie2-2.3.3.1 gmake[1]: Entering directory '/construction/biology/bowtie2/bowtie2-2.3.3.1' c++ -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -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/usr/local/include -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 diff_sample.cpp bowtie_build_main.cpp \ -lz -lpthread -L/usr/local/lib -ltbb -ltbbmalloc c++ -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -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/usr/local/include -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 diff_sample.cpp bowtie_build_main.cpp \ -lz -lpthread -L/usr/local/lib -ltbb -ltbbmalloc c++ -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -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/usr/local/include -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 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 \ -lz -lpthread -L/usr/local/lib -ltbb -ltbbmalloc c++ -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -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/usr/local/include -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 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 \ -lz -lpthread -L/usr/local/lib -ltbb -ltbbmalloc c++ -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops \ -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -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/usr/local/include -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 \ -lz -lpthread -L/usr/local/lib -ltbb -ltbbmalloc In file included from bt2_idx.h:42:0, from bt2_build.cpp:28: blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = SString; TIndexOffU = unsigned int]': bt2_build.cpp:684:1: required from here blockwise_sa.h:262:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < _sampleSuffs.size() + 1; i++) { ^ blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = S2bDnaString; TIndexOffU = unsigned int]': bt2_build.cpp:684:1: required from here blockwise_sa.h:262:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] In file included from bt2_idx.h:42:0, from bt2_build.cpp:28: blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = SString; TIndexOffU = long unsigned int]': bt2_build.cpp:684:1: required from here blockwise_sa.h:262:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < _sampleSuffs.size() + 1; i++) { ^ blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = S2bDnaString; TIndexOffU = long unsigned int]': bt2_build.cpp:684:1: required from here blockwise_sa.h:262:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] c++ -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops \ -DCOMPILER_OPTIONS="\" -pipe -O2 -fno-strict-aliasing -msse2 -funroll-loops -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -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/usr/local/include -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 \ -lz -lpthread -L/usr/local/lib -ltbb -ltbbmalloc 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 '/construction/biology/bowtie2/bowtie2-2.3.3.1' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> bowtie2-2.3.3.1 depends on file: /usr/local/bin/python2.7 - found ===> bowtie2-2.3.3.1 depends on package: perl5>=5.26<5.27 - not found ===> Installing existing package /packages/All/perl5-5.26.1.txz Installing perl5-5.26.1... Extracting perl5-5.26.1: .......... done Message from perl5-5.26.1: 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. ===> bowtie2-2.3.3.1 depends on package: perl5>=5.26<5.27 - found ===> Returning to build of bowtie2-2.3.3.1 -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for bowtie2-2.3.3.1 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/bowtie2/bowtie2-2.3.3.1' mkdir -p /construction/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 /construction/biology/bowtie2/stage/usr/local/bin ; \ done gmake[1]: Leaving directory '/construction/biology/bowtie2/bowtie2-2.3.3.1' /bin/mkdir -p /construction/biology/bowtie2/stage/usr/local/share/bowtie2/scripts install -s -m 555 /construction/biology/bowtie2/bowtie2-2.3.3.1/bowtie2*-s /construction/biology/bowtie2/bowtie2-2.3.3.1/bowtie2*-l /construction/biology/bowtie2/stage/usr/local/bin install -m 555 /construction/biology/bowtie2/bowtie2-2.3.3.1/scripts/*.sh /construction/biology/bowtie2/bowtie2-2.3.3.1/scripts/*.pl /construction/biology/bowtie2/stage/usr/local/share/bowtie2/scripts (cd /construction/biology/bowtie2/bowtie2-2.3.3.1/doc && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /construction/biology/bowtie2/stage/usr/local/share/doc/bowtie2) (cd /construction/biology/bowtie2/bowtie2-2.3.3.1/example && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /construction/biology/bowtie2/stage/usr/local/share/examples/bowtie2) ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for bowtie2-2.3.3.1 file sizes/checksums [66]: . done packing files [66]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 18 APR 2018 at 02:07:35 UTC Duration: 00:04:49