------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/libyaml-0.2.5.txz Installing /packages/All/ncurses-6.2.20200831.txz Installing /packages/All/libedit-3.1.20191231,1.txz Installing /packages/All/libunwind-20200331_1.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/ruby-2.6.6_1,1.txz ===== Message from ruby-2.6.6_1,1: -- Some of the standard commands are provided as separate ports for ease of upgrading: devel/ruby-gems: gem - RubyGems package manager devel/rubygem-irb: irb - Interactive Ruby devel/rubygem-rake: rake - Ruby Make devel/rubygem-rdoc: rdoc - Ruby Documentation System And some of the standard libraries are provided as separate ports since they require extra dependencies: databases/rubygem-dbm: DBM module databases/rubygem-gdbm: GDBM module Install them as occasion demands. Installing /packages/All/yaggo-1.5.9.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/pkgconf-1.7.3,1.txz Installing /packages/All/libtextstyle-0.21.txz Installing /packages/All/gettext-tools-0.21.txz Installing /packages/All/m4-1.4.18_1,1.txz Installing /packages/All/autoconf-wrapper-20131203.txz Installing /packages/All/perl5-5.32.0.txz Installing /packages/All/autoconf-2.69_3.txz Installing /packages/All/automake-1.16.2.txz Installing /packages/All/libtool-2.4.6_1.txz Installing /packages/All/libdeflate-1.6.txz Installing /packages/All/libnghttp2-1.41.0.txz Installing /packages/All/ca_root_nss-3.56.txz ===== Message from ca_root_nss-3.56: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem Installing /packages/All/curl-7.72.0.txz Installing /packages/All/htslib-1.10.2.txz SUCCEEDED 00:00:15 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> Jellyfish-2.2.10_9 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> Jellyfish-2.2.10_9 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by Jellyfish-2.2.10_9 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> Jellyfish-2.2.10_9 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by Jellyfish-2.2.10_9 for building => SHA256 Checksum OK for gmarcais-Jellyfish-v2.2.10_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> Jellyfish-2.2.10_9 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by Jellyfish-2.2.10_9 for building ===> Extracting for Jellyfish-2.2.10_9 ===> Jellyfish-2.2.10_9 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by Jellyfish-2.2.10_9 for building => SHA256 Checksum OK for gmarcais-Jellyfish-v2.2.10_GH0.tar.gz. Extracted Memory Use: 2.93M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for Jellyfish-2.2.10_9 ===> Applying ports patches for Jellyfish-2.2.10_9 from /xports/biology/jellyfish/files /usr/bin/env WRKSRC=/construction/biology/jellyfish/Jellyfish-2.2.10 REWARNFILE=/construction/biology/jellyfish/reinplace_warnings.txt /xports/Mk/Scripts/sed_checked.sh -e 's@Werror@Wno-deprecated-declarations@g' /construction/biology/jellyfish/Jellyfish-2.2.10/development.mk SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> Jellyfish-2.2.10_9 depends on executable: yaggo - found ===> Jellyfish-2.2.10_9 depends on package: gmake>=4.3 - found ===> Jellyfish-2.2.10_9 depends on package: pkgconf>=1.3.0_1 - found ===> Jellyfish-2.2.10_9 depends on executable: msgfmt - found ===> Jellyfish-2.2.10_9 depends on package: autoconf>=2.69 - found ===> Jellyfish-2.2.10_9 depends on package: automake>=1.16.1 - found ===> Jellyfish-2.2.10_9 depends on executable: libtoolize - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> Jellyfish-2.2.10_9 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Jellyfish-2.2.10_9 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> Jellyfish-2.2.10_9 depends on executable: yaggo - found ===> Jellyfish-2.2.10_9 depends on package: gmake>=4.3 - found ===> Jellyfish-2.2.10_9 depends on package: pkgconf>=1.3.0_1 - found ===> Jellyfish-2.2.10_9 depends on executable: msgfmt - found ===> Jellyfish-2.2.10_9 depends on package: autoconf>=2.69 - found ===> Jellyfish-2.2.10_9 depends on package: automake>=1.16.1 - found ===> Jellyfish-2.2.10_9 depends on executable: libtoolize - found ===> Jellyfish-2.2.10_9 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Jellyfish-2.2.10_9 depends on shared library: libintl.so - found (/usr/local/lib/libintl.so) ===> Configuring for Jellyfish-2.2.10_9 libtoolize: putting auxiliary files in '.'. libtoolize: copying file './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:8: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' configure: WARNING: unrecognized options: --enable-nls configure: loading site script /xports/Templates/config.site checking build system type... x86_64-portbld-dragonfly5.9 checking host system type... x86_64-portbld-dragonfly5.9 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 gmake supports nested variables... (cached) yes checking how to print strings... printf checking whether gmake supports the include directive... yes (GNU style) 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 dependency style of cc... gcc3 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-dragonfly5.9 file names to x86_64-portbld-dragonfly5.9 format... func_convert_file_noop checking how to convert x86_64-portbld-dragonfly5.9 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... dragonfly5.9 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 for ld... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for shared library run path origin... done checking pkg-config is at least version 0.9.0... yes checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 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... dragonfly5.9 ld.so checking how to hardcode library paths into programs... immediate checking 32-bit host C ABI... no checking for ELF binary format... yes checking for the common suffixes of directories in the library search path... lib,lib,lib checking for HTSLIB... no checking for samtools... no checking for md5sum... no checking for md5... md5 -r checking for yaggo... /usr/local/bin/yaggo checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for x86 cpuid 0x00000000 output... 14:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x80000000 output... 80000008:0:0:0 checking for x86 cpuid 0x00000001 output... 406f1:1c100800:7ffefbff:bfebfbff checking for x86 cpuid 0x00000007 output... 0:21cbfbb:0:0 checking for x86 cpuid 0x80000001 output... 0:0:121:2c100800 checking for x86-AVX xgetbv 0x00000000 output... 7:0 checking whether RDRND is supported by the processor... yes checking whether RDRND is supported by the processor and OS... yes checking whether C++ compiler accepts -mrdrnd... yes checking whether BMI1 is supported by the processor... yes checking whether BMI1 is supported by the processor and OS... yes checking whether C++ compiler accepts -mbmi... yes checking whether BMI2 is supported by the processor... yes checking whether BMI2 is supported by the processor and OS... yes checking whether C++ compiler accepts -mbmi2... yes checking whether ADX is supported by the processor... yes checking whether ADX is supported by the processor and OS... yes checking whether C++ compiler accepts -madx... yes checking whether MPX is supported by the processor... no checking whether PREFETCHWT1 is supported by the processor... no checking whether ABM is supported by the processor... yes checking whether ABM is supported by the processor and OS... yes checking whether C++ compiler accepts -mabm... yes checking whether MMX is supported by the processor... yes checking whether MMX is supported by the processor and OS... yes checking whether C++ compiler accepts -mmmx... yes checking whether SSE is supported by the processor... yes checking whether SSE is supported by the processor and OS... yes checking whether C++ compiler accepts -msse... yes checking whether SSE2 is supported by the processor... yes checking whether SSE2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse2... yes checking whether SSE3 is supported by the processor... yes checking whether SSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse3... yes checking whether SSSE3 is supported by the processor... yes checking whether SSSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mssse3... yes checking whether SSE4.1 is supported by the processor... yes checking whether SSE4.1 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.1... yes checking whether SSE4.2 is supported by the processor... yes checking whether SSE4.2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.2... yes checking whether SSE4a is supported by the processor... no checking whether SHA is supported by the processor... no checking whether AES is supported by the processor... yes checking whether AES is supported by the processor and OS... yes checking whether C++ compiler accepts -maes... yes checking whether AVX is supported by the processor... yes checking whether AVX is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx... yes checking whether FMA3 is supported by the processor... yes checking whether FMA3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mfma... yes checking whether FMA4 is supported by the processor... no checking whether XOP is supported by the processor... no checking whether AVX2 is supported by the processor... yes checking whether AVX2 is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx2... yes checking whether AVX512-F is supported by the processor... no checking whether AVX512-CD is supported by the processor... no checking whether AVX512-PF is supported by the processor... no checking whether AVX512-ER is supported by the processor... no checking whether AVX512-VL is supported by the processor... no checking whether AVX512-BW is supported by the processor... no checking whether AVX512-DQ is supported by the processor... no checking whether AVX512-IFMA is supported by the processor... no checking whether AVX512-VBMI is supported by the processor... no checking for __int128... yes checking for std::numeric_limits<__int128>... no checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... yes checking for sys/syscall.h... yes checking for siginfo_t.si_int... no checking for posix_memalign... yes checking for aligned_alloc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating tests/compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --enable-nls SUCCEEDED 00:00:23 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for Jellyfish-2.2.10_9 gmake[2]: Entering directory '/construction/biology/jellyfish/Jellyfish-2.2.10' /usr/local/bin/yaggo --license ./header-license -o sub_commands/count_main_cmdline.hpp sub_commands/count_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/info_main_cmdline.hpp sub_commands/info_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/dump_main_cmdline.hpp sub_commands/dump_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/histo_main_cmdline.hpp sub_commands/histo_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/stats_main_cmdline.hpp sub_commands/stats_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/merge_main_cmdline.hpp sub_commands/merge_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/bc_main_cmdline.hpp sub_commands/bc_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/query_main_cmdline.hpp sub_commands/query_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/cite_main_cmdline.hpp sub_commands/cite_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o sub_commands/mem_main_cmdline.hpp sub_commands/mem_main_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o jellyfish/generate_sequence_cmdline.hpp jellyfish/generate_sequence_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o jellyfish/fastq2sam_cmdline.hpp jellyfish/fastq2sam_cmdline.yaggo /usr/local/bin/yaggo --license ./header-license -o unit_tests/test_main_cmdline.hpp unit_tests/test_main_cmdline.yaggo gmake all-am gmake[3]: Entering directory '/construction/biology/jellyfish/Jellyfish-2.2.10' depbase=`echo sub_commands/jellyfish.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/jellyfish.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/count_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/count_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/count_main.o sub_commands/count_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/info_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/info_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/info_main.o sub_commands/info_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/dump_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/dump_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/dump_main.o sub_commands/dump_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/histo_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/histo_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/histo_main.o sub_commands/histo_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/stats_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/stats_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/stats_main.o sub_commands/stats_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/merge_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/merge_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/merge_main.o sub_commands/merge_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/bc_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/bc_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/bc_main.o sub_commands/bc_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/query_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/query_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/query_main.o sub_commands/query_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/cite_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/cite_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/cite_main.o sub_commands/cite_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo sub_commands/mem_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT sub_commands/mem_main.o -MD -MP -MF $depbase.Tpo -c -o sub_commands/mem_main.o sub_commands/mem_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo jellyfish/merge_files.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT jellyfish/merge_files.o -MD -MP -MF $depbase.Tpo -c -o jellyfish/merge_files.o jellyfish/merge_files.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo lib/rectangular_binary_matrix.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT lib/rectangular_binary_matrix.lo -MD -MP -MF $depbase.Tpo -c -o lib/rectangular_binary_matrix.lo lib/rectangular_binary_matrix.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -MT lib/rectangular_binary_matrix.lo -MD -MP -MF lib/.deps/rectangular_binary_matrix.Tpo -c lib/rectangular_binary_matrix.cc -fPIC -DPIC -o lib/.libs/rectangular_binary_matrix.o depbase=`echo lib/mer_dna.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include 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lib/generator_manager.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libjellyfish-2.0.a libtool: link: ( cd ".libs" && rm -f "libjellyfish-2.0.la" && ln -s "../libjellyfish-2.0.la" "libjellyfish-2.0.la" ) /bin/sh ./libtool --tag=CXX --mode=link c++ -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -pthread -o bin/jellyfish sub_commands/jellyfish.o sub_commands/count_main.o sub_commands/info_main.o sub_commands/dump_main.o sub_commands/histo_main.o sub_commands/stats_main.o sub_commands/merge_main.o sub_commands/bc_main.o sub_commands/query_main.o sub_commands/cite_main.o sub_commands/mem_main.o jellyfish/merge_files.o libjellyfish-2.0.la libtool: link: c++ -Wno-deprecated-declarations -std=c++11 -pipe -O2 -fno-strict-aliasing -faligned-new -pthread -o bin/.libs/jellyfish sub_commands/jellyfish.o sub_commands/count_main.o sub_commands/info_main.o sub_commands/dump_main.o sub_commands/histo_main.o sub_commands/stats_main.o sub_commands/merge_main.o sub_commands/bc_main.o sub_commands/query_main.o sub_commands/cite_main.o sub_commands/mem_main.o jellyfish/merge_files.o ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/usr/local/lib gmake[3]: Leaving directory '/construction/biology/jellyfish/Jellyfish-2.2.10' gmake[2]: Leaving directory '/construction/biology/jellyfish/Jellyfish-2.2.10' SUCCEEDED 00:00:14 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for Jellyfish-2.2.10_9 ===> Generating temporary packing list gmake[2]: Entering directory '/construction/biology/jellyfish/Jellyfish-2.2.10' if test -z 'strip'; then \ gmake INSTALL_PROGRAM="/bin/sh /construction/biology/jellyfish/Jellyfish-2.2.10/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /construction/biology/jellyfish/Jellyfish-2.2.10/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ install; \ else \ gmake INSTALL_PROGRAM="/bin/sh /construction/biology/jellyfish/Jellyfish-2.2.10/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /construction/biology/jellyfish/Jellyfish-2.2.10/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ "INSTALL_PROGRAM_ENV=STRIPPROG='strip'" install; \ fi gmake[3]: Entering directory '/construction/biology/jellyfish/Jellyfish-2.2.10' gmake install-am gmake[4]: Entering directory '/construction/biology/jellyfish/Jellyfish-2.2.10' gmake[5]: Entering directory '/construction/biology/jellyfish/Jellyfish-2.2.10' /bin/mkdir -p '/construction/biology/jellyfish/stage/usr/local/lib' /bin/sh ./libtool --mode=install /usr/bin/install -c -s libjellyfish-2.0.la '/construction/biology/jellyfish/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /construction/biology/jellyfish/stage/usr/local/lib/libjellyfish-2.0.so.2.0.0 libtool: install: strip --strip-unneeded /construction/biology/jellyfish/stage/usr/local/lib/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /construction/biology/jellyfish/stage/usr/local/lib && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /construction/biology/jellyfish/stage/usr/local/lib && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /construction/biology/jellyfish/stage/usr/local/lib/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /construction/biology/jellyfish/stage/usr/local/lib/libjellyfish-2.0.a libtool: install: strip --strip-debug /construction/biology/jellyfish/stage/usr/local/lib/libjellyfish-2.0.a libtool: install: chmod 644 /construction/biology/jellyfish/stage/usr/local/lib/libjellyfish-2.0.a libtool: install: ranlib /construction/biology/jellyfish/stage/usr/local/lib/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/local/lib' /bin/mkdir -p '/construction/biology/jellyfish/stage/usr/local/bin' STRIPPROG='strip' /bin/sh ./libtool --mode=install /bin/sh /construction/biology/jellyfish/Jellyfish-2.2.10/install-sh -c -s bin/jellyfish '/construction/biology/jellyfish/stage/usr/local/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/jellyfish/Jellyfish-2.2.10/install-sh -c -s bin/.libs/jellyfish /construction/biology/jellyfish/stage/usr/local/bin/jellyfish /bin/mkdir -p '/construction/biology/jellyfish/stage/usr/local/include/jellyfish-2.2.10/jellyfish' install -m 0644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/construction/biology/jellyfish/stage/usr/local/include/jellyfish-2.2.10/jellyfish' install -m 0644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/construction/biology/jellyfish/stage/usr/local/include/jellyfish-2.2.10/jellyfish' /bin/mkdir -p '/construction/biology/jellyfish/stage/usr/local/man/man1' install -m 0644 'doc/jellyfish.man' '/construction/biology/jellyfish/stage/usr/local/man/man1/jellyfish.1' /bin/mkdir -p '/construction/biology/jellyfish/stage/usr/local/libdata/pkgconfig' install -m 0644 jellyfish-2.0.pc '/construction/biology/jellyfish/stage/usr/local/libdata/pkgconfig' gmake[5]: Leaving directory '/construction/biology/jellyfish/Jellyfish-2.2.10' gmake[4]: Leaving directory '/construction/biology/jellyfish/Jellyfish-2.2.10' gmake[3]: Leaving directory '/construction/biology/jellyfish/Jellyfish-2.2.10' gmake[2]: Leaving directory '/construction/biology/jellyfish/Jellyfish-2.2.10' ====> 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: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for Jellyfish-2.2.10_9 file sizes/checksums [57]: 0% file sizes/checksums [57]: 100% packing files [57]: 0% packing files [57]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:00:55