=>> Building biology/fastx-toolkit build started at Thu Dec 11 20:41:23 EST 2025 port directory: /usr/ports/biology/fastx-toolkit package name: fastx_toolkit-0.0.14_1 building for: FreeBSD pkg.DaveG.ca 13.5-RELEASE-p7 FreeBSD 13.5-RELEASE-p7 1305000 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 573 Aug 27 2024 /usr/ports/biology/fastx-toolkit/Makefile Ports top last git commit: 62d8b1999233 Ports top unclean checkout: no Port dir last git commit: d89248272808 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1305000 Job Id: 06 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p7 1305000 UNAME_r=13.5-RELEASE-p7 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=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/06/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_13_5_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_13_5_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 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=/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 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=/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=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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=13.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.0 PERL_VER=5.42 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/5.42 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--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 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 #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---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-2.4.2_1.pkg [pkg.DaveG.ca] Installing pkg-2.4.2_1... [pkg.DaveG.ca] Extracting pkg-2.4.2_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-2.4.3,1.pkg [pkg.DaveG.ca] Installing pkgconf-2.4.3,1... [pkg.DaveG.ca] Extracting pkgconf-2.4.3,1: .......... 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.DaveG.ca] Installing autoconf-2.72... [pkg.DaveG.ca] `-- Installing autoconf-switch-20220527... [pkg.DaveG.ca] `-- Extracting autoconf-switch-20220527: ....... done [pkg.DaveG.ca] `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Installing m4-1.4.20,1... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.23.1... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.23.1: .......... done [pkg.DaveG.ca] `-- Extracting m4-1.4.20,1: .......... done [pkg.DaveG.ca] `-- Installing perl5-5.42.0_1... [pkg.DaveG.ca] `-- Extracting perl5-5.42.0_1: .......... done [pkg.DaveG.ca] Extracting autoconf-2.72: .......... done ===> 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>=1.17 - not found ===> Installing existing package /packages/All/automake-1.17.pkg [pkg.DaveG.ca] Installing automake-1.17... [pkg.DaveG.ca] Extracting automake-1.17: .......... done ===> fastx_toolkit-0.0.14_1 depends on package: automake>=1.17 - 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-2.5.4_1.pkg [pkg.DaveG.ca] Installing libtool-2.5.4_1... [pkg.DaveG.ca] Extracting libtool-2.5.4_1: .......... done ===> fastx_toolkit-0.0.14_1 depends on executable: libtoolize - found ===> Returning to build of fastx_toolkit-0.0.14_1 ===> fastx_toolkit-0.0.14_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> fastx_toolkit-0.0.14_1 depends on file: /usr/local/bin/ccache - 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.DaveG.ca] Installing libgtextutils-0.7... [pkg.DaveG.ca] 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. aclocal.m4:1058: 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 sleep supports fractional seconds... yes checking filesystem timestamp resolution... 2 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 xargs -n works... 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-freebsd13.5 checking host system type... amd64-portbld-freebsd13.5 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-freebsd13.5 file names to amd64-portbld-freebsd13.5 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd13.5 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... objdump 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 ranlib... ranlib checking for ar... ar checking for archiver @FILE support... no checking for strip... strip 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... freebsd13.5 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... freebsd13.5 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 --- all --- /usr/bin/make all-recursive --- all-recursive --- Making all in m4 Making all in src --- all-recursive --- Making all in libfastx --- chomp.o --- --- fastx.o --- --- fastx_args.o --- --- sequence_alignment.o --- --- chomp.o --- 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 --- fastx_args.o --- 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 --- fastx.o --- 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 --- sequence_alignment.o --- 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 --- chomp.o --- mv -f .deps/chomp.Tpo .deps/chomp.Po --- fastx_args.o --- mv -f .deps/fastx_args.Tpo .deps/fastx_args.Po --- fastx.o --- mv -f .deps/fastx.Tpo .deps/fastx.Po --- sequence_alignment.o --- mv -f .deps/sequence_alignment.Tpo .deps/sequence_alignment.Po --- libfastx.a --- rm -f libfastx.a ar cr libfastx.a chomp.o fastx.o fastx_args.o sequence_alignment.o ranlib libfastx.a Making all in fastx_clipper --- fastx_clipper.o --- 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 --- fastx_clipper --- /bin/sh ../../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -o fastx_clipper fastx_clipper.o ../libfastx/libfastx.a libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -o fastx_clipper fastx_clipper.o ../libfastx/libfastx.a Making all in fastx_trimmer --- fastx_trimmer.o --- 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 --- fastx_trimmer --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -o fastx_trimmer fastx_trimmer.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -o fastx_trimmer fastx_trimmer.o ../libfastx/libfastx.a Making all in fastx_quality_stats --- fastx_quality_stats.o --- 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 --- fastx_quality_stats --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -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 -o fastx_quality_stats fastx_quality_stats.o ../libfastx/libfastx.a Making all in fastq_quality_converter --- fastq_quality_converter.o --- 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 --- fastq_quality_converter --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -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 -o fastq_quality_converter fastq_quality_converter.o ../libfastx/libfastx.a Making all in fastq_to_fasta --- fastq_to_fasta.o --- 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 --- fastq_to_fasta --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -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 -o fastq_to_fasta fastq_to_fasta.o ../libfastx/libfastx.a Making all in fastq_quality_filter --- fastq_quality_filter.o --- 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 --- fastq_quality_filter --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -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 -o fastq_quality_filter fastq_quality_filter.o ../libfastx/libfastx.a Making all in fastq_quality_trimmer --- fastq_quality_trimmer.o --- 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 --- fastq_quality_trimmer --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -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 -o fastq_quality_trimmer fastq_quality_trimmer.o ../libfastx/libfastx.a Making all in fastx_artifacts_filter --- fastx_artifacts_filter.o --- 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 --- fastx_artifacts_filter --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -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 -o fastx_artifacts_filter fastx_artifacts_filter.o ../libfastx/libfastx.a Making all in fastx_reverse_complement --- fastx_reverse_complement.o --- 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 --- fastx_reverse_complement --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -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 -o fastx_reverse_complement fastx_reverse_complement.o ../libfastx/libfastx.a Making all in fastx_collapser --- fastx_collapser.o --- 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 --- fastx_collapser --- /bin/sh ../../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -o fastx_collapser fastx_collapser.o ../libfastx/libfastx.a libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -o fastx_collapser fastx_collapser.o ../libfastx/libfastx.a Making all in fastx_uncollapser --- fastx_uncollapser.o --- 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 --- fastx_uncollapser --- /bin/sh ../../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -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 -o fastx_uncollapser fastx_uncollapser.o -L/usr/local/lib -lgtextutils ../libfastx/libfastx.a Making all in seqalign_test --- seqalign_test.o --- 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 --- seqalign_test --- /bin/sh ../../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -o seqalign_test seqalign_test.o ../libfastx/libfastx.a libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -o seqalign_test seqalign_test.o ../libfastx/libfastx.a Making all in fasta_formatter --- fasta_formatter.o --- 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 --- fasta_formatter --- /bin/sh ../../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -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 -o fasta_formatter fasta_formatter.o -L/usr/local/lib -lgtextutils ../libfastx/libfastx.a Making all in fasta_nucleotide_changer --- fasta_nucleotide_changer.o --- 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 --- fasta_nucleotide_changer --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -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 -o fasta_nucleotide_changer fasta_nucleotide_changer.o ../libfastx/libfastx.a Making all in fastx_renamer --- fastx_renamer.o --- 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 --- fastx_renamer --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -o fastx_renamer fastx_renamer.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -o fastx_renamer fastx_renamer.o ../libfastx/libfastx.a Making all in fastq_masker --- fastq_masker.o --- 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 --- fastq_masker --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -o fastq_masker fastq_masker.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DDEBUG -g -O1 -o fastq_masker fastq_masker.o ../libfastx/libfastx.a Making all in doc Making all in galaxy --- all-recursive --- Making all in tools --- all-recursive --- Making all in fastx_toolkit Making all in test-data Making all in static --- all-recursive --- 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>=5.42.r<5.43 - 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=2025-12-12T01:41:23+0000' 'PKG_NOTE_ports_top_git_hash=62d8b1999233' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=d89248272808' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' 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 Dec 11 20:43:20 EST 2025 build time: 00:01:59