------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> The following configuration options are available for bowtie2-2.4.2_3: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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/python3.7" 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=gcc80 CMAKE_PREFIX_PATH="/usr/local" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/bowtie2/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_EXT_SUFFIX= PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 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/5.32 PROFILE="@comment " DOCSDIR="share/doc/bowtie2" EXAMPLESDIR="share/examples/bowtie2" DATADIR="share/bowtie2" WWWDIR="www/bowtie2" ETCDIR="etc/bowtie2" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: 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 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600100 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/expat-2.2.10.txz Installing /packages/All/ncurses-6.2.20210313_1.txz ===== Message from ncurses-6.2.20210313_1: -- { type: install message: < bowtie2-2.4.2_3 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> bowtie2-2.4.2_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bowtie2-2.4.2_3 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> bowtie2-2.4.2_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bowtie2-2.4.2_3 for building => SHA256 Checksum OK for BenLangmead-bowtie2-v2.4.2_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> bowtie2-2.4.2_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bowtie2-2.4.2_3 for building ===> Extracting for bowtie2-2.4.2_3 => SHA256 Checksum OK for BenLangmead-bowtie2-v2.4.2_GH0.tar.gz. Extracted Memory Use: 25.18M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for bowtie2-2.4.2_3 ===> Applying ports patches for bowtie2-2.4.2_3 from /xports/biology/bowtie2/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> bowtie2-2.4.2_3 depends on package: gmake>=4.3 - found ===> bowtie2-2.4.2_3 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> bowtie2-2.4.2_3 depends on shared library: libtbb.so - found (/usr/local/lib/libtbb.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> bowtie2-2.4.2_3 depends on package: gmake>=4.3 - found ===> bowtie2-2.4.2_3 depends on file: /usr/local/bin/python3.7 - found ===> bowtie2-2.4.2_3 depends on shared library: libtbb.so - found (/usr/local/lib/libtbb.so) ===> Configuring for bowtie2-2.4.2_3 SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for bowtie2-2.4.2_3 gmake[1]: Entering directory '/construction/biology/bowtie2/bowtie2-2.4.2' c++ -DCOMPILER_OPTIONS="\" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -isystem /usr/local/include -I third_party \ -o bowtie2-build-s bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -L/usr/local/lib -lz -lpthread -ltbb -ltbbmalloc c++ -DCOMPILER_OPTIONS="\" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -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 \ -isystem /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 \ -L/usr/local/lib -lz -lpthread -ltbb -ltbbmalloc c++ -DCOMPILER_OPTIONS="\" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -isystem /usr/local/include -I third_party \ -o bowtie2-align-s bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -L/usr/local/lib -lz -lpthread -ltbb -ltbbmalloc c++ -DCOMPILER_OPTIONS="\" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -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 \ -isystem /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 \ -L/usr/local/lib -lz -lpthread -ltbb -ltbbmalloc c++ \ -DCOMPILER_OPTIONS="\" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`c++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \ -isystem /usr/local/include -I third_party \ -o bowtie2-inspect-s bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \ -L/usr/local/lib -lz -lpthread -ltbb -ltbbmalloc c++ \ -DCOMPILER_OPTIONS="\" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -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 \ -isystem /usr/local/include -I third_party \ -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 \ -L/usr/local/lib -lz -lpthread -ltbb -ltbbmalloc In file included from aligner_seed2.cpp:22: 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:1019:10: 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; ^~~~ In file included from aligner_seed2.cpp:22: 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:1019:10: 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/bowtie2-2.4.2' SUCCEEDED 00:05:08 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> bowtie2-2.4.2_3 depends on executable: bash - found ===> bowtie2-2.4.2_3 depends on file: /usr/local/bin/python3.7 - found ===> bowtie2-2.4.2_3 depends on package: perl5>=5.32.r0<5.33 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for bowtie2-2.4.2_3 ===> bowtie2-2.4.2_3 depends on executable: bash - found ===> bowtie2-2.4.2_3 depends on file: /usr/local/bin/python3.7 - found ===> bowtie2-2.4.2_3 depends on package: perl5>=5.32.r0<5.33 - found ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/bowtie2/bowtie2-2.4.2' 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/bowtie2-2.4.2' install -s -m 555 /construction/biology/bowtie2/bowtie2-2.4.2/bowtie2*-s /construction/biology/bowtie2/bowtie2-2.4.2/bowtie2*-l /construction/biology/bowtie2/stage/usr/local/bin install -m 555 /construction/biology/bowtie2/bowtie2-2.4.2/scripts/*.sh /construction/biology/bowtie2/bowtie2-2.4.2/scripts/*.pl /construction/biology/bowtie2/stage/usr/local/share/bowtie2/scripts install -m 555 /construction/biology/bowtie2/bowtie2-test /construction/biology/bowtie2/stage/usr/local/bin (cd /construction/biology/bowtie2/bowtie2-2.4.2/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/bowtie2-2.4.2/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) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> 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) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for bowtie2-2.4.2_3 file sizes/checksums [67]: 0% file sizes/checksums [67]: 100% packing files [67]: 0% packing files [67]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:28 TOTAL TIME 00:06:15