=>> Building biology/fastx-toolkit build started at Thu Apr 4 18:47:14 BST 2024 port directory: /usr/ports/biology/fastx-toolkit package name: fastx_toolkit-0.0.14_1 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 573 Mar 8 2023 /usr/ports/biology/fastx-toolkit/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c014f9c79a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 04 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work/.cache HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/fastx-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fastx-toolkit/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.72 CCACHE_DIR="/root/.ccache" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work/.cache HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/fastx-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fastx-toolkit/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DEFAULT_AUTOCONF=2.72 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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" --End MAKE_ENV-- --PLIST_SUB-- OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 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/5.36 DOCSDIR="share/doc/fastx_toolkit" EXAMPLESDIR="share/examples/fastx_toolkit" DATADIR="share/fastx_toolkit" WWWDIR="www/fastx_toolkit" ETCDIR="etc/fastx_toolkit" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fastx_toolkit DOCSDIR=/usr/local/share/doc/fastx_toolkit EXAMPLESDIR=/usr/local/share/examples/fastx_toolkit WWWDIR=/usr/local/www/fastx_toolkit ETCDIR=/usr/local/etc/fastx_toolkit --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fastx_toolkit-0.0.14_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> fastx_toolkit-0.0.14_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of fastx_toolkit-0.0.14_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by fastx_toolkit-0.0.14_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by fastx_toolkit-0.0.14_1 for building => SHA256 Checksum OK for agordon-fastx_toolkit-0.0.14_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by fastx_toolkit-0.0.14_1 for building ===> Extracting for fastx_toolkit-0.0.14_1 => SHA256 Checksum OK for agordon-fastx_toolkit-0.0.14_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for fastx_toolkit-0.0.14_1 ===> Applying FreeBSD patches for fastx_toolkit-0.0.14_1 from /usr/ports/biology/fastx-toolkit/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fastx_toolkit-0.0.14_1 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.1.1,1.pkg [pkg-builder.dan.net.uk] Installing pkgconf-2.1.1,1... [pkg-builder.dan.net.uk] Extracting pkgconf-2.1.1,1: .......... done ===> fastx_toolkit-0.0.14_1 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of fastx_toolkit-0.0.14_1 ===> fastx_toolkit-0.0.14_1 depends on package: autoconf>=2.72 - not found ===> Installing existing package /packages/All/autoconf-2.72.pkg [pkg-builder.dan.net.uk] Installing autoconf-2.72... [pkg-builder.dan.net.uk] `-- Installing autoconf-switch-20220527... [pkg-builder.dan.net.uk] `-- Extracting autoconf-switch-20220527: ....... done [pkg-builder.dan.net.uk] `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Installing m4-1.4.19_1,1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libsigsegv-2.14... [pkg-builder.dan.net.uk] | `-- Extracting libsigsegv-2.14: ..... done [pkg-builder.dan.net.uk] `-- Extracting m4-1.4.19_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing perl5-5.36.3_1... [pkg-builder.dan.net.uk] `-- Extracting perl5-5.36.3_1: .......... done [pkg-builder.dan.net.uk] Extracting autoconf-2.72: .......... done ===== Message from libsigsegv-2.14: -- Note that the stackoverflow handling functions of this library need procfs mounted on /proc. ===> fastx_toolkit-0.0.14_1 depends on package: autoconf>=2.72 - found ===> Returning to build of fastx_toolkit-0.0.14_1 ===> fastx_toolkit-0.0.14_1 depends on package: automake>=1.16.5 - not found ===> Installing existing package /packages/All/automake-1.16.5_1.pkg [pkg-builder.dan.net.uk] Installing automake-1.16.5_1... [pkg-builder.dan.net.uk] Extracting automake-1.16.5_1: .......... done ===> fastx_toolkit-0.0.14_1 depends on package: automake>=1.16.5 - found ===> Returning to build of fastx_toolkit-0.0.14_1 ===> fastx_toolkit-0.0.14_1 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.4.7_2.pkg [pkg-builder.dan.net.uk] Installing libtool-2.4.7_2... [pkg-builder.dan.net.uk] Extracting libtool-2.4.7_2: .......... done ===> fastx_toolkit-0.0.14_1 depends on executable: libtoolize - found ===> Returning to build of fastx_toolkit-0.0.14_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fastx_toolkit-0.0.14_1 depends on shared library: libgtextutils.so - not found ===> Installing existing package /packages/All/libgtextutils-0.7.pkg [pkg-builder.dan.net.uk] Installing libgtextutils-0.7... [pkg-builder.dan.net.uk] Extracting libgtextutils-0.7: .......... done ===> fastx_toolkit-0.0.14_1 depends on shared library: libgtextutils.so - found (/usr/local/lib/libgtextutils.so) ===> Returning to build of fastx_toolkit-0.0.14_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for fastx_toolkit-0.0.14_1 libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:17: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.ac:17: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:1089: AM_CONFIG_HEADER is expanded from... configure.ac:17: the top level configure.ac:22: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:22: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:22: the top level configure.ac:23: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.ac:23: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... m4/ax_c_long_long.m4:26: AX_C_LONG_LONG is expanded from... configure.ac:23: the top level configure.ac:24: warning: The macro 'AC_LANG_CPLUSPLUS' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/c.m4:270: AC_LANG_CPLUSPLUS is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... m4/ax_cxx_header_stdcxx_tr1.m4:29: AX_CXX_HEADER_STDCXX_TR1 is expanded from... configure.ac:24: the top level configure.ac:24: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.ac:24: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... m4/ax_cxx_header_stdcxx_tr1.m4:29: AX_CXX_HEADER_STDCXX_TR1 is expanded from... configure.ac:24: the top level configure.ac:20: installing 'config/compile' configure.ac:22: installing 'config/config.guess' configure.ac:22: installing 'config/config.sub' configure.ac:18: installing 'config/install-sh' configure.ac:18: installing 'config/missing' src/fasta_formatter/Makefile.am: installing 'config/depcomp' configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of cc... gcc3 checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking dependency style of c++... gcc3 checking build system type... amd64-portbld-freebsd13.2 checking host system type... amd64-portbld-freebsd13.2 checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... (cached) /usr/bin/fgrep checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 524288 checking how to convert amd64-portbld-freebsd13.2 file names to amd64-portbld-freebsd13.2 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd13.2 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... no checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from cc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd13.2 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... c++ -E checking for ld used by c++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... yes checking if c++ supports -c -o file.o... yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd13.2 ld.so checking how to hardcode library paths into programs... immediate checking for long long int... yes checking for ISO C++ TR1 include files... no checking whether c++ supports C++11 features by default... yes checking pkg-config is at least version 0.9.0... yes checking for gtextutils... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating m4/Makefile config.status: creating src/Makefile config.status: creating src/libfastx/Makefile config.status: creating src/fastx_clipper/Makefile config.status: creating src/fastq_to_fasta/Makefile config.status: creating src/fastx_quality_stats/Makefile config.status: creating src/fastq_quality_converter/Makefile config.status: creating src/fastx_trimmer/Makefile config.status: creating src/fastq_quality_filter/Makefile config.status: creating src/fastq_quality_trimmer/Makefile config.status: creating src/fastx_artifacts_filter/Makefile config.status: creating src/fastx_reverse_complement/Makefile config.status: creating src/fastx_collapser/Makefile config.status: creating src/fastx_uncollapser/Makefile config.status: creating src/seqalign_test/Makefile config.status: creating src/fasta_formatter/Makefile config.status: creating src/fasta_nucleotide_changer/Makefile config.status: creating src/fastx_renamer/Makefile config.status: creating src/fastq_masker/Makefile config.status: creating galaxy/Makefile config.status: creating galaxy/tools/Makefile config.status: creating galaxy/tools/fastx_toolkit/Makefile config.status: creating galaxy/test-data/Makefile config.status: creating galaxy/static/Makefile config.status: creating galaxy/static/fastx_icons/Makefile config.status: creating galaxy/tool-data/Makefile config.status: creating scripts/Makefile config.status: creating build_scripts/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for fastx_toolkit-0.0.14_1 /usr/bin/make all-recursive Making all in m4 Making all in src Making all in libfastx cc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT chomp.o -MD -MP -MF .deps/chomp.Tpo -c -o chomp.o chomp.c mv -f .deps/chomp.Tpo .deps/chomp.Po cc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastx.o -MD -MP -MF .deps/fastx.Tpo -c -o fastx.o fastx.c mv -f .deps/fastx.Tpo .deps/fastx.Po cc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastx_args.o -MD -MP -MF .deps/fastx_args.Tpo -c -o fastx_args.o fastx_args.c mv -f .deps/fastx_args.Tpo .deps/fastx_args.Po c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT sequence_alignment.o -MD -MP -MF .deps/sequence_alignment.Tpo -c -o sequence_alignment.o sequence_alignment.cpp mv -f .deps/sequence_alignment.Tpo .deps/sequence_alignment.Po rm -f libfastx.a ar cru libfastx.a chomp.o fastx.o fastx_args.o sequence_alignment.o ranlib libfastx.a Making all in fastx_clipper c++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastx_clipper.o -MD -MP -MF .deps/fastx_clipper.Tpo -c -o fastx_clipper.o fastx_clipper.cpp mv -f .deps/fastx_clipper.Tpo .deps/fastx_clipper.Po /bin/sh ../../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_clipper fastx_clipper.o ../libfastx/libfastx.a libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_clipper fastx_clipper.o ../libfastx/libfastx.a Making all in fastx_trimmer cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastx_trimmer.o -MD -MP -MF .deps/fastx_trimmer.Tpo -c -o fastx_trimmer.o fastx_trimmer.c mv -f .deps/fastx_trimmer.Tpo .deps/fastx_trimmer.Po /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_trimmer fastx_trimmer.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_trimmer fastx_trimmer.o ../libfastx/libfastx.a Making all in fastx_quality_stats cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastx_quality_stats.o -MD -MP -MF .deps/fastx_quality_stats.Tpo -c -o fastx_quality_stats.o fastx_quality_stats.c mv -f .deps/fastx_quality_stats.Tpo .deps/fastx_quality_stats.Po /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_quality_stats fastx_quality_stats.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_quality_stats fastx_quality_stats.o ../libfastx/libfastx.a Making all in fastq_quality_converter cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastq_quality_converter.o -MD -MP -MF .deps/fastq_quality_converter.Tpo -c -o fastq_quality_converter.o fastq_quality_converter.c mv -f .deps/fastq_quality_converter.Tpo .deps/fastq_quality_converter.Po /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastq_quality_converter fastq_quality_converter.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastq_quality_converter fastq_quality_converter.o ../libfastx/libfastx.a Making all in fastq_to_fasta cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastq_to_fasta.o -MD -MP -MF .deps/fastq_to_fasta.Tpo -c -o fastq_to_fasta.o fastq_to_fasta.c mv -f .deps/fastq_to_fasta.Tpo .deps/fastq_to_fasta.Po /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastq_to_fasta fastq_to_fasta.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastq_to_fasta fastq_to_fasta.o ../libfastx/libfastx.a Making all in fastq_quality_filter cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastq_quality_filter.o -MD -MP -MF .deps/fastq_quality_filter.Tpo -c -o fastq_quality_filter.o fastq_quality_filter.c mv -f .deps/fastq_quality_filter.Tpo .deps/fastq_quality_filter.Po /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastq_quality_filter fastq_quality_filter.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastq_quality_filter fastq_quality_filter.o ../libfastx/libfastx.a Making all in fastq_quality_trimmer cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastq_quality_trimmer.o -MD -MP -MF .deps/fastq_quality_trimmer.Tpo -c -o fastq_quality_trimmer.o fastq_quality_trimmer.c mv -f .deps/fastq_quality_trimmer.Tpo .deps/fastq_quality_trimmer.Po /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastq_quality_trimmer fastq_quality_trimmer.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastq_quality_trimmer fastq_quality_trimmer.o ../libfastx/libfastx.a Making all in fastx_artifacts_filter cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastx_artifacts_filter.o -MD -MP -MF .deps/fastx_artifacts_filter.Tpo -c -o fastx_artifacts_filter.o fastx_artifacts_filter.c mv -f .deps/fastx_artifacts_filter.Tpo .deps/fastx_artifacts_filter.Po /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_artifacts_filter fastx_artifacts_filter.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_artifacts_filter fastx_artifacts_filter.o ../libfastx/libfastx.a Making all in fastx_reverse_complement cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastx_reverse_complement.o -MD -MP -MF .deps/fastx_reverse_complement.Tpo -c -o fastx_reverse_complement.o fastx_reverse_complement.c mv -f .deps/fastx_reverse_complement.Tpo .deps/fastx_reverse_complement.Po /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_reverse_complement fastx_reverse_complement.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_reverse_complement fastx_reverse_complement.o ../libfastx/libfastx.a Making all in fastx_collapser c++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastx_collapser.o -MD -MP -MF .deps/fastx_collapser.Tpo -c -o fastx_collapser.o fastx_collapser.cpp mv -f .deps/fastx_collapser.Tpo .deps/fastx_collapser.Po /bin/sh ../../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_collapser fastx_collapser.o ../libfastx/libfastx.a libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_collapser fastx_collapser.o ../libfastx/libfastx.a Making all in fastx_uncollapser c++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include/gtextutils -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastx_uncollapser.o -MD -MP -MF .deps/fastx_uncollapser.Tpo -c -o fastx_uncollapser.o fastx_uncollapser.cpp mv -f .deps/fastx_uncollapser.Tpo .deps/fastx_uncollapser.Po /bin/sh ../../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_uncollapser fastx_uncollapser.o -L/usr/local/lib -lgtextutils ../libfastx/libfastx.a libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_uncollapser fastx_uncollapser.o -L/usr/local/lib -lgtextutils ../libfastx/libfastx.a Making all in seqalign_test c++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT seqalign_test.o -MD -MP -MF .deps/seqalign_test.Tpo -c -o seqalign_test.o seqalign_test.cpp mv -f .deps/seqalign_test.Tpo .deps/seqalign_test.Po /bin/sh ../../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o seqalign_test seqalign_test.o ../libfastx/libfastx.a libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o seqalign_test seqalign_test.o ../libfastx/libfastx.a Making all in fasta_formatter c++ -DHAVE_CONFIG_H -I. -I../.. -I/usr/local/include/gtextutils -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fasta_formatter.o -MD -MP -MF .deps/fasta_formatter.Tpo -c -o fasta_formatter.o fasta_formatter.cpp mv -f .deps/fasta_formatter.Tpo .deps/fasta_formatter.Po /bin/sh ../../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fasta_formatter fasta_formatter.o -L/usr/local/lib -lgtextutils ../libfastx/libfastx.a libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fasta_formatter fasta_formatter.o -L/usr/local/lib -lgtextutils ../libfastx/libfastx.a Making all in fasta_nucleotide_changer cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fasta_nucleotide_changer.o -MD -MP -MF .deps/fasta_nucleotide_changer.Tpo -c -o fasta_nucleotide_changer.o fasta_nucleotide_changer.c mv -f .deps/fasta_nucleotide_changer.Tpo .deps/fasta_nucleotide_changer.Po /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fasta_nucleotide_changer fasta_nucleotide_changer.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fasta_nucleotide_changer fasta_nucleotide_changer.o ../libfastx/libfastx.a Making all in fastx_renamer cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastx_renamer.o -MD -MP -MF .deps/fastx_renamer.Tpo -c -o fastx_renamer.o fastx_renamer.c mv -f .deps/fastx_renamer.Tpo .deps/fastx_renamer.Po /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_renamer fastx_renamer.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastx_renamer fastx_renamer.o ../libfastx/libfastx.a Making all in fastq_masker cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -MT fastq_masker.o -MD -MP -MF .deps/fastq_masker.Tpo -c -o fastq_masker.o fastq_masker.c mv -f .deps/fastq_masker.Tpo .deps/fastq_masker.Po /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastq_masker fastq_masker.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -fstack-protector-strong -o fastq_masker fastq_masker.o ../libfastx/libfastx.a Making all in doc Making all in galaxy Making all in tools Making all in fastx_toolkit Making all in test-data Making all in static Making all in fastx_icons Making all in tool-data Making all in scripts Making all in build_scripts =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fastx_toolkit-0.0.14_1 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for fastx_toolkit-0.0.14_1 ===> Generating temporary packing list Making install in m4 /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/share/aclocal' install -m 0644 ax_c_long_long.m4 ax_cxx_compile_stdcxx_11.m4 ax_cxx_header_stdcxx_tr1.m4 '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/share/aclocal' Making install in src Making install in libfastx Making install in fastx_clipper /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_clipper '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_clipper /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fastx_clipper Making install in fastx_trimmer /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_trimmer '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_trimmer /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fastx_trimmer Making install in fastx_quality_stats /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_quality_stats '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_quality_stats /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fastx_quality_stats Making install in fastq_quality_converter /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastq_quality_converter '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fastq_quality_converter /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fastq_quality_converter Making install in fastq_to_fasta /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastq_to_fasta '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fastq_to_fasta /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fastq_to_fasta Making install in fastq_quality_filter /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastq_quality_filter '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fastq_quality_filter /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fastq_quality_filter Making install in fastq_quality_trimmer /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastq_quality_trimmer '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fastq_quality_trimmer /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fastq_quality_trimmer Making install in fastx_artifacts_filter /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_artifacts_filter '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_artifacts_filter /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fastx_artifacts_filter Making install in fastx_reverse_complement /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_reverse_complement '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_reverse_complement /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fastx_reverse_complement Making install in fastx_collapser /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_collapser '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_collapser /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fastx_collapser Making install in fastx_uncollapser /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_uncollapser '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_uncollapser /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fastx_uncollapser Making install in seqalign_test Making install in fasta_formatter /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fasta_formatter '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fasta_formatter /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fasta_formatter Making install in fasta_nucleotide_changer /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fasta_nucleotide_changer '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fasta_nucleotide_changer /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fasta_nucleotide_changer Making install in fastx_renamer /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_renamer '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_renamer /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fastx_renamer Making install in fastq_masker /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastq_masker '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' libtool: install: install -m 555 -s fastq_masker /wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin/fastq_masker Making install in doc Making install in galaxy Making install in tools Making install in fastx_toolkit Making install in test-data Making install in static Making install in fastx_icons Making install in tool-data Making install in scripts /bin/mkdir -p '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' install -m 555 fastx_barcode_splitter.pl fastx_nucleotide_distribution_graph.sh fastx_nucleotide_distribution_line_graph.sh fastq_quality_boxplot_graph.sh fasta_clipping_histogram.pl '/wrkdirs/usr/ports/biology/fastx-toolkit/work/stage/usr/local/bin' Making install in build_scripts ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-04-04T17:47:14+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=c014f9c79a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for fastx_toolkit-0.0.14_1 ===> Building fastx_toolkit-0.0.14_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for fastx_toolkit-0.0.14_1 build of biology/fastx-toolkit | fastx_toolkit-0.0.14_1 ended at Thu Apr 4 18:48:00 BST 2024 build time: 00:00:47