------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.20.2.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/pkgconf-1.6.3,1.txz Installing /packages/All/m4-1.4.18_1,1.txz Installing /packages/All/autoconf-wrapper-20131203.txz Installing /packages/All/perl5-5.30.3.txz ===== Message from perl5-5.30.3: -- 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. Installing /packages/All/autoconf-2.69_3.txz Installing /packages/All/automake-1.16.2.txz SUCCEEDED 00:00:16 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> vcftools-0.1.16 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> vcftools-0.1.16 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by vcftools-0.1.16 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> vcftools-0.1.16 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by vcftools-0.1.16 for building => SHA256 Checksum OK for vcftools-vcftools-v0.1.16_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> vcftools-0.1.16 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by vcftools-0.1.16 for building ===> Extracting for vcftools-0.1.16 => SHA256 Checksum OK for vcftools-vcftools-v0.1.16_GH0.tar.gz. Extracted Memory Use: 1.41M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for vcftools-0.1.16 ===> Applying dragonfly patches for vcftools-0.1.16 from /xports/biology/vcftools/dragonfly SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> vcftools-0.1.16 depends on package: gmake>=4.3 - found ===> vcftools-0.1.16 depends on package: pkgconf>=1.3.0_1 - found ===> vcftools-0.1.16 depends on package: autoconf>=2.69 - found ===> vcftools-0.1.16 depends on package: automake>=1.16.1 - found ===> vcftools-0.1.16 depends on package: perl5>=5.30.r1<5.31 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> vcftools-0.1.16 depends on package: gmake>=4.3 - found ===> vcftools-0.1.16 depends on package: pkgconf>=1.3.0_1 - found ===> vcftools-0.1.16 depends on package: autoconf>=2.69 - found ===> vcftools-0.1.16 depends on package: automake>=1.16.1 - found ===> vcftools-0.1.16 depends on package: perl5>=5.30.r1<5.31 - found ===> Configuring for vcftools-0.1.16 configure.ac:16: installing './compile' configure.ac:12: installing './install-sh' configure.ac:12: installing './missing' src/cpp/Makefile.am: installing './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 gmake sets $(MAKE)... yes checking whether gmake supports nested variables... yes 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 c++ accepts -g... yes checking whether gmake supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking for gcc... cc 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 dependency style of cc... gcc3 checking how to run the C preprocessor... cpp checking for perl... (cached) /usr/local/bin/perl checking pkg-config is at least version 0.9.0... yes checking for ZLIB... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep 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 arpa/inet.h... (cached) yes checking for fcntl.h... (cached) yes checking for limits.h... (cached) yes checking for netdb.h... (cached) yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for sys/socket.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for inline... inline checking for int16_t... (cached) yes checking for int32_t... (cached) yes checking for int64_t... (cached) yes checking for int8_t... (cached) yes checking for off_t... (cached) yes checking for size_t... (cached) yes checking for ssize_t... (cached) yes checking for uint16_t... (cached) yes checking for uint32_t... (cached) yes checking for uint8_t... (cached) yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for error_at_line... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for gethostbyaddr... yes checking for gethostbyname... (cached) yes checking for memset... (cached) yes checking for pow... no checking for select... (cached) yes checking for socket... yes checking for sqrt... no checking for strchr... (cached) yes checking for strdup... (cached) yes checking for strerror... (cached) yes checking for strstr... (cached) yes checking for strtol... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/cpp/Makefile config.status: creating src/perl/Makefile config.status: creating config.h config.status: executing depfiles commands SUCCEEDED 00:00:26 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for vcftools-0.1.16 gmake[1]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16' gmake all-recursive gmake[2]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16' Making all in src gmake[3]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16/src' Making all in cpp gmake[4]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16/src/cpp' c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-bcf_entry.o -MD -MP -MF .deps/vcftools-bcf_entry.Tpo -c -o vcftools-bcf_entry.o `test -f 'bcf_entry.cpp' || echo './'`bcf_entry.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-bcf_entry_setters.o -MD -MP -MF .deps/vcftools-bcf_entry_setters.Tpo -c -o vcftools-bcf_entry_setters.o `test -f 'bcf_entry_setters.cpp' || echo './'`bcf_entry_setters.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-bcf_file.o -MD -MP -MF .deps/vcftools-bcf_file.Tpo -c -o vcftools-bcf_file.o `test -f 'bcf_file.cpp' || echo './'`bcf_file.cpp cc -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-bgzf.o -MD -MP -MF .deps/vcftools-bgzf.Tpo -c -o vcftools-bgzf.o `test -f 'bgzf.c' || echo './'`bgzf.c c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-dgeev.o -MD -MP -MF .deps/vcftools-dgeev.Tpo -c -o vcftools-dgeev.o `test -f 'dgeev.cpp' || echo './'`dgeev.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-entry.o -MD -MP -MF .deps/vcftools-entry.Tpo -c -o vcftools-entry.o `test -f 'entry.cpp' || echo './'`entry.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-entry_filters.o -MD -MP -MF .deps/vcftools-entry_filters.Tpo -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-entry_getters.o -MD -MP -MF .deps/vcftools-entry_getters.Tpo -c -o vcftools-entry_getters.o `test -f 'entry_getters.cpp' || echo './'`entry_getters.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-entry_setters.o -MD -MP -MF .deps/vcftools-entry_setters.Tpo -c -o vcftools-entry_setters.o `test -f 'entry_setters.cpp' || echo './'`entry_setters.cpp c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-gamma.o -MD -MP -MF .deps/vcftools-gamma.Tpo -c -o vcftools-gamma.o `test -f 'gamma.cpp' || echo './'`gamma.cpp mv -f .deps/vcftools-dgeev.Tpo .deps/vcftools-dgeev.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-header.o -MD -MP -MF .deps/vcftools-header.Tpo -c -o vcftools-header.o `test -f 'header.cpp' || echo './'`header.cpp mv -f .deps/vcftools-bgzf.Tpo .deps/vcftools-bgzf.Po cc -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-knetfile.o -MD -MP -MF .deps/vcftools-knetfile.Tpo -c -o vcftools-knetfile.o `test -f 'knetfile.c' || echo './'`knetfile.c mv -f .deps/vcftools-knetfile.Tpo .deps/vcftools-knetfile.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-output_log.o -MD -MP -MF .deps/vcftools-output_log.Tpo -c -o vcftools-output_log.o `test -f 'output_log.cpp' || echo './'`output_log.cpp mv -f .deps/vcftools-gamma.Tpo .deps/vcftools-gamma.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-parameters.o -MD -MP -MF .deps/vcftools-parameters.Tpo -c -o vcftools-parameters.o `test -f 'parameters.cpp' || echo './'`parameters.cpp mv -f .deps/vcftools-entry_setters.Tpo .deps/vcftools-entry_setters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-variant_file.o -MD -MP -MF .deps/vcftools-variant_file.Tpo -c -o vcftools-variant_file.o `test -f 'variant_file.cpp' || echo './'`variant_file.cpp mv -f .deps/vcftools-entry_getters.Tpo .deps/vcftools-entry_getters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-variant_file_diff.o -MD -MP -MF .deps/vcftools-variant_file_diff.Tpo -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp mv -f .deps/vcftools-entry.Tpo .deps/vcftools-entry.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-variant_file_filters.o -MD -MP -MF .deps/vcftools-variant_file_filters.Tpo -c -o vcftools-variant_file_filters.o `test -f 'variant_file_filters.cpp' || echo './'`variant_file_filters.cpp mv -f .deps/vcftools-output_log.Tpo .deps/vcftools-output_log.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-variant_file_format_convert.o -MD -MP -MF .deps/vcftools-variant_file_format_convert.Tpo -c -o vcftools-variant_file_format_convert.o `test -f 'variant_file_format_convert.cpp' || echo './'`variant_file_format_convert.cpp mv -f .deps/vcftools-bcf_entry_setters.Tpo .deps/vcftools-bcf_entry_setters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-variant_file_output.o -MD -MP -MF .deps/vcftools-variant_file_output.Tpo -c -o vcftools-variant_file_output.o `test -f 'variant_file_output.cpp' || echo './'`variant_file_output.cpp mv -f .deps/vcftools-entry_filters.Tpo .deps/vcftools-entry_filters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-vcf_entry.o -MD -MP -MF .deps/vcftools-vcf_entry.Tpo -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp mv -f .deps/vcftools-variant_file.Tpo .deps/vcftools-variant_file.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-vcf_entry_setters.o -MD -MP -MF .deps/vcftools-vcf_entry_setters.Tpo -c -o vcftools-vcf_entry_setters.o `test -f 'vcf_entry_setters.cpp' || echo './'`vcf_entry_setters.cpp mv -f .deps/vcftools-variant_file_filters.Tpo .deps/vcftools-variant_file_filters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-vcf_file.o -MD -MP -MF .deps/vcftools-vcf_file.Tpo -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp mv -f .deps/vcftools-parameters.Tpo .deps/vcftools-parameters.Po c++ -DHAVE_CONFIG_H -I. -I../.. -pipe -O2 -fno-strict-aliasing -MT vcftools-vcftools.o -MD -MP -MF .deps/vcftools-vcftools.Tpo -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp mv -f .deps/vcftools-bcf_file.Tpo .deps/vcftools-bcf_file.Po mv -f .deps/vcftools-header.Tpo .deps/vcftools-header.Po mv -f .deps/vcftools-variant_file_diff.Tpo .deps/vcftools-variant_file_diff.Po mv -f .deps/vcftools-vcftools.Tpo .deps/vcftools-vcftools.Po mv -f .deps/vcftools-variant_file_format_convert.Tpo .deps/vcftools-variant_file_format_convert.Po mv -f .deps/vcftools-vcf_entry_setters.Tpo .deps/vcftools-vcf_entry_setters.Po mv -f .deps/vcftools-bcf_entry.Tpo .deps/vcftools-bcf_entry.Po mv -f .deps/vcftools-vcf_file.Tpo .deps/vcftools-vcf_file.Po mv -f .deps/vcftools-vcf_entry.Tpo .deps/vcftools-vcf_entry.Po mv -f .deps/vcftools-variant_file_output.Tpo .deps/vcftools-variant_file_output.Po c++ -pipe -O2 -fno-strict-aliasing -o vcftools vcftools-bcf_entry.o vcftools-bcf_entry_setters.o vcftools-bcf_file.o vcftools-bgzf.o vcftools-dgeev.o vcftools-entry.o vcftools-entry_filters.o vcftools-entry_getters.o vcftools-entry_setters.o vcftools-gamma.o vcftools-header.o vcftools-knetfile.o vcftools-output_log.o vcftools-parameters.o vcftools-variant_file.o vcftools-variant_file_diff.o vcftools-variant_file_filters.o vcftools-variant_file_format_convert.o vcftools-variant_file_output.o vcftools-vcf_entry.o vcftools-vcf_entry_setters.o vcftools-vcf_file.o vcftools-vcftools.o -lz gmake[4]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16/src/cpp' Making all in perl gmake[4]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16/src/perl' gmake[4]: Nothing to be done for 'all'. gmake[4]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16/src/perl' gmake[4]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16/src' gmake[4]: Nothing to be done for 'all-am'. gmake[4]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16/src' gmake[3]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16/src' gmake[3]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16' gmake[3]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16' gmake[2]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16' gmake[1]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16' SUCCEEDED 00:00:41 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> vcftools-0.1.16 depends on package: perl5>=5.30.r1<5.31 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for vcftools-0.1.16 ===> vcftools-0.1.16 depends on package: perl5>=5.30.r1<5.31 - found ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16' Making install in src gmake[2]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16/src' Making install in cpp gmake[3]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16/src/cpp' gmake[4]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16/src/cpp' /bin/mkdir -p '/construction/biology/vcftools/stage/usr/local/bin' install -s -m 555 vcftools '/construction/biology/vcftools/stage/usr/local/bin' /bin/mkdir -p '/construction/biology/vcftools/stage/usr/local/man/man1' install -m 0644 vcftools.1 '/construction/biology/vcftools/stage/usr/local/man/man1' gmake[4]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16/src/cpp' gmake[3]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16/src/cpp' Making install in perl gmake[3]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16/src/perl' gmake[4]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16/src/perl' /bin/mkdir -p '/construction/biology/vcftools/stage/usr/local/bin' install -m 555 fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare vcf-concat vcf-consensus vcf-contrast vcf-convert vcf-fix-newlines vcf-fix-ploidy vcf-indel-stats vcf-isec vcf-merge vcf-phased-join vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab vcf-tstv vcf-validator '/construction/biology/vcftools/stage/usr/local/bin' /bin/mkdir -p '/construction/biology/vcftools/stage/usr/local/lib/perl5/site_perl' install -m 0644 FaSlice.pm Vcf.pm VcfStats.pm '/construction/biology/vcftools/stage/usr/local/lib/perl5/site_perl' gmake[4]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16/src/perl' gmake[3]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16/src/perl' gmake[3]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16/src' gmake[4]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16/src' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16/src' gmake[3]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16/src' gmake[2]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16/src' gmake[2]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16' gmake[3]: Entering directory '/construction/biology/vcftools/vcftools-0.1.16' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16' gmake[2]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16' gmake[1]: Leaving directory '/construction/biology/vcftools/vcftools-0.1.16' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for vcftools-0.1.16 file sizes/checksums [29]: 0% file sizes/checksums [29]: 100% packing files [29]: 0% packing files [29]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:03 TOTAL TIME 00:01:29