Created attachment 161349 [details] SHAR archive The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. WWW: http://hannonlab.cshl.edu/fastx_toolkit/
Hi, Jason. There is problem with building of this port: =======================<phase: configure >============================ ===> Configuring for fastx_toolkit-0.0.14 configure.ac:22: error: possibly undefined macro: AC_PROG_LIBTOOL If this token and others are legitimate, please use m4_pattern_allow. See the Autoconf documentation. autoreconf-2.69: /usr/local/bin/autoconf-2.69 failed with exit status: 1 *** Error code 1 Stop. make: stopped in /usr/ports/biology/fastx-toolkit Would you check it please?
Hi Ruslan, I can't reproduce this error. I tested on 10.1-{amd64|i386} and 9.3-amd64 and it installs cleanly on all of them. Output of "make configure" is included below. What platform are you using? Are your packages all up-to-date? Thanks much, Jason ===> License AGPLv3 accepted by the user ===> fastx_toolkit-0.0.14 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by fastx_toolkit-0.0.14 for building ===> Extracting for fastx_toolkit-0.0.14 => SHA256 Checksum OK for agordon-fastx_toolkit-0.0.14_GH0.tar.bz2. ===> Patching for fastx_toolkit-0.0.14 ===> fastx_toolkit-0.0.14 depends on executable: autoconf-2.69 - found ===> fastx_toolkit-0.0.14 depends on executable: autoheader-2.69 - found ===> fastx_toolkit-0.0.14 depends on executable: autoreconf-2.69 - found ===> fastx_toolkit-0.0.14 depends on executable: aclocal-1.15 - found ===> fastx_toolkit-0.0.14 depends on executable: automake-1.15 - found ===> fastx_toolkit-0.0.14 depends on executable: pkgconf - found ===> fastx_toolkit-0.0.14 depends on shared library: libgtextutils.so - found (/usr/local/lib/libgtextutils.so) ===> 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 /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 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 for style of include used by make... GNU 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... amd64-portbld-freebsd10.1 checking host system type... amd64-portbld-freebsd10.1 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/local/bin/nm -B checking the name lister (/usr/local/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 amd64-portbld-freebsd10.1 file names to amd64-portbld-freebsd10.1 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd10.1 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/local/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... 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... freebsd10.1 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... freebsd10.1 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
I already fixed that - it needs USES=libtool. I assume you have not tested it in clean environment (like poudriere jail), so this is why you didn't catch that :)
I tested in poudriere on 10.1-i386 and current-amd64 with latest ports tree.
You're right, I forgot to test in a clean env even though it's on my checklist. Thanks for the help...
A commit references this bug: Author: rm Date: Fri Sep 25 18:33:20 UTC 2015 New revision: 397847 URL: https://svnweb.freebsd.org/changeset/ports/397847 Log: The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. WWW: http://hannonlab.cshl.edu/fastx_toolkit/ PR: 203318 Submitted by: Jason Bacon <jwbacon@tds.net> Changes: head/biology/Makefile head/biology/fastx-toolkit/ head/biology/fastx-toolkit/Makefile head/biology/fastx-toolkit/distinfo head/biology/fastx-toolkit/pkg-descr head/biology/fastx-toolkit/pkg-plist
Committed, thank you!