=> Building biology/fastx-toolkit Started : Thursday, 30 AUG 2018 at 13:01:02 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- 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=/construction/biology/fastx-toolkit XDG_CONFIG_HOME=/construction/biology/fastx-toolkit HOME=/construction/biology/fastx-toolkit TMPDIR="/tmp" PATH=/construction/biology/fastx-toolkit/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/fastx-toolkit XDG_CONFIG_HOME=/construction/biology/fastx-toolkit HOME=/construction/biology/fastx-toolkit TMPDIR="/tmp" PATH=/construction/biology/fastx-toolkit/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/fastx-toolkit/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.26.2 PERL_VER=5.26 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.26 PROFILE="@comment " DOCSDIR="share/doc/fastx_toolkit" EXAMPLESDIR="share/examples/fastx_toolkit" DATADIR="share/fastx_toolkit" WWWDIR="www/fastx_toolkit" ETCDIR="etc/fastx_toolkit" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License AGPLv3+ accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> fastx_toolkit-0.0.14 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> fastx_toolkit-0.0.14 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of fastx_toolkit-0.0.14 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License AGPLv3+ accepted by the user ===> Fetching all distfiles required by fastx_toolkit-0.0.14 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License AGPLv3+ accepted by the user ===> Fetching all distfiles required by fastx_toolkit-0.0.14 for building => SHA256 Checksum OK for agordon-fastx_toolkit-0.0.14_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License AGPLv3+ accepted by the user ===> Fetching all distfiles required by fastx_toolkit-0.0.14 for building ===> Extracting for fastx_toolkit-0.0.14 ===> License AGPLv3+ accepted by the user ===> Fetching all distfiles required by fastx_toolkit-0.0.14 for building => SHA256 Checksum OK for agordon-fastx_toolkit-0.0.14_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for fastx_toolkit-0.0.14 ===> Applying ports patches for fastx_toolkit-0.0.14 /usr/bin/sed -i.bak -e 's/-Werror[[:>:]]//g' /construction/biology/fastx-toolkit/fastx_toolkit-0.0.14/configure.ac -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> fastx_toolkit-0.0.14 depends on package: autoconf>=2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69_1.txz Installing autoconf-2.69_1... `-- Installing autoconf-wrapper-20131203... `-- Extracting autoconf-wrapper-20131203: .......... done `-- Installing indexinfo-0.3.1... `-- Extracting indexinfo-0.3.1: .... done `-- Installing m4-1.4.18,1... `-- Extracting m4-1.4.18,1: .......... done `-- Installing perl5-5.26.2... `-- Extracting perl5-5.26.2: .......... done Extracting autoconf-2.69_1: .......... done Message from perl5-5.26.2: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> fastx_toolkit-0.0.14 depends on package: autoconf>=2.69 - found ===> Returning to build of fastx_toolkit-0.0.14 ===> fastx_toolkit-0.0.14 depends on package: automake>=1.16.1 - not found ===> Installing existing package /packages/All/automake-1.16.1.txz Installing automake-1.16.1... Extracting automake-1.16.1: .......... done ===> fastx_toolkit-0.0.14 depends on package: automake>=1.16.1 - found ===> Returning to build of fastx_toolkit-0.0.14 ===> fastx_toolkit-0.0.14 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.4.6.txz Installing libtool-2.4.6... Extracting libtool-2.4.6: .......... done ===> fastx_toolkit-0.0.14 depends on executable: libtoolize - found ===> Returning to build of fastx_toolkit-0.0.14 ===> fastx_toolkit-0.0.14 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-1.4.2,1.txz Installing pkgconf-1.4.2,1... Extracting pkgconf-1.4.2,1: .......... done ===> fastx_toolkit-0.0.14 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of fastx_toolkit-0.0.14 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> fastx_toolkit-0.0.14 depends on shared library: libgtextutils.so - not found ===> Installing existing package /packages/All/libgtextutils-0.7.txz Installing libgtextutils-0.7... Extracting libgtextutils-0.7: .......... done ===> fastx_toolkit-0.0.14 depends on shared library: libgtextutils.so - found (/usr/local/lib/libgtextutils.so) ===> Returning to build of fastx_toolkit-0.0.14 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for fastx_toolkit-0.0.14 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: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 /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe 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 we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... 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 we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking build system type... x86_64-portbld-dragonfly5.3 checking host system type... x86_64-portbld-dragonfly5.3 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 -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 262144 checking how to convert x86_64-portbld-dragonfly5.3 file names to x86_64-portbld-dragonfly5.3 format... func_convert_file_noop checking how to convert x86_64-portbld-dragonfly5.3 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r 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 ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B 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 how to run the C preprocessor... cpp checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.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... no 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... dragonfly5.3 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... dragonfly5.3 ld.so checking how to hardcode library paths into programs... immediate checking for long long int... yes checking for ISO C++ TR1 include files... yes checking whether c++ supports C++11 features by default... no checking whether c++ supports C++11 features with -std=c++11... 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 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for fastx_toolkit-0.0.14 --- 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../.. -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -MT chomp.o -MD -MP -MF .deps/chomp.Tpo -c -o chomp.o chomp.c --- fastx.o --- cc -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -MT fastx.o -MD -MP -MF .deps/fastx.Tpo -c -o fastx.o fastx.c --- fastx_args.o --- cc -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -MT fastx_args.o -MD -MP -MF .deps/fastx_args.Tpo -c -o fastx_args.o fastx_args.c --- sequence_alignment.o --- c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 cru libfastx.a chomp.o fastx.o fastx_args.o sequence_alignment.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfastx.a Making all in fastx_clipper --- fastx_clipper.o --- c++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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++ -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o fastx_clipper fastx_clipper.o ../libfastx/libfastx.a libtool: link: c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o fastx_trimmer fastx_trimmer.o ../libfastx/libfastx.a libtool: link: cc -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o fastx_quality_stats fastx_quality_stats.o ../libfastx/libfastx.a libtool: link: cc -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o fastq_quality_converter fastq_quality_converter.o ../libfastx/libfastx.a libtool: link: cc -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o fastq_to_fasta fastq_to_fasta.o ../libfastx/libfastx.a libtool: link: cc -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o fastq_quality_filter fastq_quality_filter.o ../libfastx/libfastx.a libtool: link: cc -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o fastq_quality_trimmer fastq_quality_trimmer.o ../libfastx/libfastx.a libtool: link: cc -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o fastx_artifacts_filter fastx_artifacts_filter.o ../libfastx/libfastx.a libtool: link: cc -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 --- 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.deps/fastx_collapser.Po --- fastx_collapser --- /bin/sh ../../libtool --tag=CXX --mode=link c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o fastx_collapser fastx_collapser.o ../libfastx/libfastx.a libtool: link: c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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++ -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o fastx_uncollapser fastx_uncollapser.o -L/usr/local/lib -lgtextutils ../libfastx/libfastx.a libtool: link: c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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++ -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o seqalign_test seqalign_test.o ../libfastx/libfastx.a libtool: link: c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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++ -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o fasta_formatter fasta_formatter.o -L/usr/local/lib -lgtextutils ../libfastx/libfastx.a libtool: link: c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o fasta_nucleotide_changer fasta_nucleotide_changer.o ../libfastx/libfastx.a libtool: link: cc -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o fastx_renamer fastx_renamer.o ../libfastx/libfastx.a libtool: link: cc -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -DDEBUG -g -O1 -o fastq_masker fastq_masker.o ../libfastx/libfastx.a libtool: link: cc -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -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 -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> fastx_toolkit-0.0.14 depends on package: perl5>=5.26<5.27 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for fastx_toolkit-0.0.14 ===> Generating temporary packing list Making install in m4 /bin/mkdir -p '/construction/biology/fastx-toolkit/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 '/construction/biology/fastx-toolkit/stage/usr/local/share/aclocal' Making install in src Making install in libfastx Making install in fastx_clipper /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_clipper '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_clipper /construction/biology/fastx-toolkit/stage/usr/local/bin/fastx_clipper Making install in fastx_trimmer /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_trimmer '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_trimmer /construction/biology/fastx-toolkit/stage/usr/local/bin/fastx_trimmer Making install in fastx_quality_stats /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_quality_stats '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_quality_stats /construction/biology/fastx-toolkit/stage/usr/local/bin/fastx_quality_stats Making install in fastq_quality_converter /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastq_quality_converter '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fastq_quality_converter /construction/biology/fastx-toolkit/stage/usr/local/bin/fastq_quality_converter Making install in fastq_to_fasta /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastq_to_fasta '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fastq_to_fasta /construction/biology/fastx-toolkit/stage/usr/local/bin/fastq_to_fasta Making install in fastq_quality_filter /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastq_quality_filter '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fastq_quality_filter /construction/biology/fastx-toolkit/stage/usr/local/bin/fastq_quality_filter Making install in fastq_quality_trimmer /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastq_quality_trimmer '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fastq_quality_trimmer /construction/biology/fastx-toolkit/stage/usr/local/bin/fastq_quality_trimmer Making install in fastx_artifacts_filter /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_artifacts_filter '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_artifacts_filter /construction/biology/fastx-toolkit/stage/usr/local/bin/fastx_artifacts_filter Making install in fastx_reverse_complement /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_reverse_complement '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_reverse_complement /construction/biology/fastx-toolkit/stage/usr/local/bin/fastx_reverse_complement Making install in fastx_collapser /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_collapser '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_collapser /construction/biology/fastx-toolkit/stage/usr/local/bin/fastx_collapser Making install in fastx_uncollapser /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_uncollapser '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_uncollapser /construction/biology/fastx-toolkit/stage/usr/local/bin/fastx_uncollapser Making install in seqalign_test Making install in fasta_formatter /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fasta_formatter '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fasta_formatter /construction/biology/fastx-toolkit/stage/usr/local/bin/fasta_formatter Making install in fasta_nucleotide_changer /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fasta_nucleotide_changer '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fasta_nucleotide_changer /construction/biology/fastx-toolkit/stage/usr/local/bin/fasta_nucleotide_changer Making install in fastx_renamer /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastx_renamer '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fastx_renamer /construction/biology/fastx-toolkit/stage/usr/local/bin/fastx_renamer Making install in fastq_masker /bin/mkdir -p '/construction/biology/fastx-toolkit/stage/usr/local/bin' /bin/sh ../../libtool --mode=install install -s -m 555 fastq_masker '/construction/biology/fastx-toolkit/stage/usr/local/bin' libtool: install: install -m 555 -s fastq_masker /construction/biology/fastx-toolkit/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 '/construction/biology/fastx-toolkit/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 '/construction/biology/fastx-toolkit/stage/usr/local/bin' Making install in build_scripts find: /construction/biology/fastx-toolkit/stage/usr/local/lib/perl5/site_perl: No such file or directory ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for fastx_toolkit-0.0.14 file sizes/checksums [26]: . done packing files [26]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 13:02:23 UTC Duration: 00:01:20