------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/libyaml-0.2.5.txz Installing /packages/All/ncurses-6.2.20201017.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-1.1.1h_1,1.txz Installing /packages/All/ruby-2.6.6_2,1.txz ===== Message from ruby-2.6.6_2,1: -- 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/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 SUCCEEDED 00:00:12 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> mummer-4.0.0.b2.2_3 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> mummer-4.0.0.b2.2_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mummer-4.0.0.b2.2_3 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> mummer-4.0.0.b2.2_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mummer-4.0.0.b2.2_3 for building => SHA256 Checksum OK for mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> mummer-4.0.0.b2.2_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by mummer-4.0.0.b2.2_3 for building ===> Extracting for mummer-4.0.0.b2.2_3 => SHA256 Checksum OK for mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz. Extracted Memory Use: 62.23M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for mummer-4.0.0.b2.2_3 ===> Applying ports patches for mummer-4.0.0.b2.2_3 from /xports/biology/mummer/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> mummer-4.0.0.b2.2_3 depends on executable: yaggo - found ===> mummer-4.0.0.b2.2_3 depends on package: gmake>=4.3 - found ===> mummer-4.0.0.b2.2_3 depends on package: autoconf>=2.69 - found ===> mummer-4.0.0.b2.2_3 depends on package: automake>=1.16.1 - found ===> mummer-4.0.0.b2.2_3 depends on executable: libtoolize - found ===> mummer-4.0.0.b2.2_3 depends on package: perl5>=5.32.r0<5.33 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> mummer-4.0.0.b2.2_3 depends on executable: yaggo - found ===> mummer-4.0.0.b2.2_3 depends on package: gmake>=4.3 - found ===> mummer-4.0.0.b2.2_3 depends on package: autoconf>=2.69 - found ===> mummer-4.0.0.b2.2_3 depends on package: automake>=1.16.1 - found ===> mummer-4.0.0.b2.2_3 depends on executable: libtoolize - found ===> mummer-4.0.0.b2.2_3 depends on package: perl5>=5.32.r0<5.33 - found ===> Configuring for mummer-4.0.0.b2.2_3 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: 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... no 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 for gcc... (cached) cc checking whether we are using the GNU C compiler... (cached) yes checking whether cc accepts -g... (cached) yes checking for cc option to accept ISO C89... (cached) none needed checking whether cc understands -c and -o together... (cached) yes checking dependency style of cc... (cached) gcc3 checking for env... /usr/bin/env checking for OpenMP flag of C++ compiler... -fopenmp checking for yaggo... /usr/local/bin/yaggo checking for gnuplot... no checking for gnuplot5... no checking for gnuplot4... no checking for __int128... yes checking if std::thread::sleep_for is supported... yes checking for perl... (cached) /usr/local/bin/perl checking for Perl prefix... /usr/local checking for Perl extension include path... /usr/local/lib/perl5/5.32/mach/CORE checking for Perl extension target directory... /usr/local/lib/perl5/site_perl/mach/5.32 checking for Perl extensions C preprocessor flags... -DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -DUSE_THREAD_SAFE_LOCALE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib/perl5/5.32/mach/CORE -lperl -L/usr/local/lib -fstack-protector-strong configure: compiling with flags: CXXFLAGS=-std=c++0x -pipe -O2 -fno-strict-aliasing checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating mummer.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands SUCCEEDED 00:00:19 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for mummer-4.0.0.b2.2_3 gmake[1]: Entering directory '/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5' /usr/local/bin/yaggo -o src/umd/nucmer_cmdline.hpp src/umd/nucmer_cmdline.yaggo /usr/local/bin/yaggo -o tests/generate_sequences_cmdline.hpp tests/generate_sequences_cmdline.yaggo /usr/local/bin/yaggo -o tests/ufasta_src/dsort_cmdline.hpp tests/ufasta_src/dsort_cmdline.yaggo /usr/local/bin/yaggo -o tests/ufasta_src/sort_cmdline.hpp tests/ufasta_src/sort_cmdline.yaggo /usr/local/bin/yaggo -o tests/check_cigar_cmdline.hpp tests/check_cigar_cmdline.yaggo /usr/local/bin/yaggo -o tests/check_LCP_cmdline.hpp tests/check_LCP_cmdline.yaggo gmake all-am gmake[2]: Entering directory '/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5' sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]GNUPLOT_EXE[@],false,g' < scripts/mummerplot.pl > mummerplot && chmod a+x mummerplot sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]GNUPLOT_EXE[@],false,g' < scripts/dnadiff.pl > dnadiff && chmod a+x dnadiff sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]GNUPLOT_EXE[@],false,g' < scripts/promer.pl > promer && chmod a+x promer sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]GNUPLOT_EXE[@],false,g' < scripts/exact-tandems.sh > exact-tandems && chmod a+x exact-tandems depbase=`echo src/essaMEM/fasta.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/essaMEM/fasta.o -MD -MP -MF $depbase.Tpo -c -o src/essaMEM/fasta.o src/essaMEM/fasta.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/essaMEM/mummer.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/essaMEM/mummer.o -MD -MP -MF $depbase.Tpo -c -o src/essaMEM/mummer.o src/essaMEM/mummer.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/essaMEM/sparseSA.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/essaMEM/sparseSA.lo -MD -MP -MF $depbase.Tpo -c -o src/essaMEM/sparseSA.lo src/essaMEM/sparseSA.cpp &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo src/essaMEM/sssort_compact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/essaMEM/sssort_compact.lo -MD -MP -MF $depbase.Tpo -c -o src/essaMEM/sssort_compact.lo src/essaMEM/sssort_compact.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo src/umd/nucmer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/umd/nucmer.lo -MD -MP -MF $depbase.Tpo -c -o src/umd/nucmer.lo src/umd/nucmer.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo src/umd/nucmer_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/umd/nucmer_main.o -MD -MP -MF $depbase.Tpo -c -o src/umd/nucmer_main.o src/umd/nucmer_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/mgaps_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/mgaps_main.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/mgaps_main.o src/tigr/mgaps_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/postnuc_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/postnuc_main.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/postnuc_main.o src/tigr/postnuc_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/prepro.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/prepro.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/prepro.o src/tigr/prepro.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/postpro.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/postpro.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/postpro.o src/tigr/postpro.cc &&\ mv -f $depbase.Tpo $depbase.Po libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/umd/nucmer.lo -MD -MP -MF src/umd/.deps/nucmer.Tpo -c src/umd/nucmer.cc -fPIC -DPIC -o src/umd/.libs/nucmer.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/essaMEM/sssort_compact.lo -MD -MP -MF src/essaMEM/.deps/sssort_compact.Tpo -c src/essaMEM/sssort_compact.cc -fPIC -DPIC -o src/essaMEM/.libs/sssort_compact.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/essaMEM/sparseSA.lo -MD -MP -MF src/essaMEM/.deps/sparseSA.Tpo -c src/essaMEM/sparseSA.cpp -fPIC -DPIC -o src/essaMEM/.libs/sparseSA.o depbase=`echo src/tigr/mgaps.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/mgaps.lo -MD -MP -MF $depbase.Tpo -c -o src/tigr/mgaps.lo src/tigr/mgaps.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/mgaps.lo -MD -MP -MF src/tigr/.deps/mgaps.Tpo -c src/tigr/mgaps.cc -fPIC -DPIC -o src/tigr/.libs/mgaps.o depbase=`echo src/tigr/postnuc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/postnuc.lo -MD -MP -MF $depbase.Tpo -c -o src/tigr/postnuc.lo src/tigr/postnuc.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo src/tigr/sw_align.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/sw_align.lo -MD -MP -MF $depbase.Tpo -c -o src/tigr/sw_align.lo src/tigr/sw_align.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/postnuc.lo -MD -MP -MF src/tigr/.deps/postnuc.Tpo -c src/tigr/postnuc.cc -fPIC -DPIC -o src/tigr/.libs/postnuc.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/sw_align.lo -MD -MP -MF src/tigr/.deps/sw_align.Tpo -c src/tigr/sw_align.cc -fPIC -DPIC -o src/tigr/.libs/sw_align.o depbase=`echo src/tigr/tigrinc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/tigrinc.lo -MD -MP -MF $depbase.Tpo -c -o src/tigr/tigrinc.lo src/tigr/tigrinc.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/tigrinc.lo -MD -MP -MF src/tigr/.deps/tigrinc.Tpo -c src/tigr/tigrinc.cc -fPIC -DPIC -o src/tigr/.libs/tigrinc.o depbase=`echo src/tigr/show-coords.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/show-coords.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/show-coords.o src/tigr/show-coords.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/delta.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/delta.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/delta.o src/tigr/delta.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/show-aligns.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/show-aligns.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/show-aligns.o src/tigr/show-aligns.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/translate.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/translate.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/translate.o src/tigr/translate.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/show-snps.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/show-snps.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/show-snps.o src/tigr/show-snps.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/show-tiling.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/show-tiling.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/show-tiling.o src/tigr/show-tiling.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/show-diff.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/show-diff.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/show-diff.o src/tigr/show-diff.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/repeat-match.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/repeat-match.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/repeat-match.o src/tigr/repeat-match.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/annotate.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/annotate.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/annotate.o src/tigr/annotate.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/combineMUMs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/combineMUMs.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/combineMUMs.o src/tigr/combineMUMs.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/delta-filter.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/delta-filter.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/delta-filter.o src/tigr/delta-filter.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o libumdmummer.la -rpath /usr/local/lib src/essaMEM/sparseSA.lo src/essaMEM/sssort_compact.lo src/tigr/mgaps.lo src/tigr/postnuc.lo src/tigr/sw_align.lo src/tigr/tigrinc.lo src/umd/nucmer.lo libtool: link: c++ -fPIC -DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/gcc80/crtbeginS.o src/essaMEM/.libs/sparseSA.o src/essaMEM/.libs/sssort_compact.o src/tigr/.libs/mgaps.o src/tigr/.libs/postnuc.o src/tigr/.libs/sw_align.o src/tigr/.libs/tigrinc.o src/umd/.libs/nucmer.o -lpthread -L/usr/lib/gcc80 -lstdc++ -lm -lc -lgcc -lgcc_pic /usr/lib/gcc80/crtendS.o /usr/lib/crtn.o -fopenmp -O2 -fopenmp -Wl,-soname -Wl,libumdmummer.so.0 -o .libs/libumdmummer.so.0.0.0 libtool: link: (cd ".libs" && rm -f "libumdmummer.so.0" && ln -s "libumdmummer.so.0.0.0" "libumdmummer.so.0") libtool: link: (cd ".libs" && rm -f "libumdmummer.so" && ln -s "libumdmummer.so.0.0.0" "libumdmummer.so") libtool: link: ( cd ".libs" && rm -f "libumdmummer.la" && ln -s "../libumdmummer.la" "libumdmummer.la" ) /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o mummer src/essaMEM/fasta.o src/essaMEM/mummer.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o show-coords src/tigr/show-coords.o src/tigr/delta.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o show-aligns src/tigr/show-aligns.o src/tigr/delta.o src/tigr/translate.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o show-snps src/tigr/show-snps.o src/tigr/delta.o src/tigr/translate.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o show-tiling src/tigr/show-tiling.o src/tigr/delta.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o show-diff src/tigr/show-diff.o src/tigr/delta.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o repeat-match src/tigr/repeat-match.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o annotate src/tigr/annotate.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o combineMUMs src/tigr/combineMUMs.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o delta-filter src/tigr/delta-filter.o src/tigr/delta.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/combineMUMs src/tigr/combineMUMs.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/repeat-match src/tigr/repeat-match.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/show-tiling src/tigr/show-tiling.o src/tigr/delta.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/show-coords src/tigr/show-coords.o src/tigr/delta.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/show-aligns src/tigr/show-aligns.o src/tigr/delta.o src/tigr/translate.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/annotate src/tigr/annotate.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o nucmer src/umd/nucmer_main.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/show-snps src/tigr/show-snps.o src/tigr/delta.o src/tigr/translate.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o mgaps src/tigr/mgaps_main.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/show-diff src/tigr/show-diff.o src/tigr/delta.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o postnuc src/tigr/postnuc_main.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/mummer src/essaMEM/fasta.o src/essaMEM/mummer.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/delta-filter src/tigr/delta-filter.o src/tigr/delta.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o postpro src/tigr/postpro.o src/tigr/translate.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -lpthread -o prepro src/tigr/prepro.o src/tigr/translate.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/postnuc src/tigr/postnuc_main.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/nucmer src/umd/nucmer_main.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/prepro src/tigr/prepro.o src/tigr/translate.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/postpro src/tigr/postpro.o src/tigr/translate.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -o .libs/mgaps src/tigr/mgaps_main.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib gmake[2]: Leaving directory '/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5' gmake[1]: Leaving directory '/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5' SUCCEEDED 00:00:17 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> mummer-4.0.0.b2.2_3 depends on package: perl5>=5.32.r0<5.33 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for mummer-4.0.0.b2.2_3 ===> mummer-4.0.0.b2.2_3 depends on package: perl5>=5.32.r0<5.33 - found ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5' gmake install-am gmake[2]: Entering directory '/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5' gmake[3]: Entering directory '/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5' /bin/mkdir -p '/construction/biology/mummer/stage/usr/local/lib' /bin/sh ./libtool --mode=install /usr/bin/install -c libumdmummer.la '/construction/biology/mummer/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libumdmummer.so.0.0.0 /construction/biology/mummer/stage/usr/local/lib/libumdmummer.so.0.0.0 libtool: install: (cd /construction/biology/mummer/stage/usr/local/lib && { ln -s -f libumdmummer.so.0.0.0 libumdmummer.so.0 || { rm -f libumdmummer.so.0 && ln -s libumdmummer.so.0.0.0 libumdmummer.so.0; }; }) libtool: install: (cd /construction/biology/mummer/stage/usr/local/lib && { ln -s -f libumdmummer.so.0.0.0 libumdmummer.so || { rm -f libumdmummer.so && ln -s libumdmummer.so.0.0.0 libumdmummer.so; }; }) libtool: install: /usr/bin/install -c .libs/libumdmummer.lai /construction/biology/mummer/stage/usr/local/lib/libumdmummer.la libtool: warning: remember to run 'libtool --finish /usr/local/lib' /bin/mkdir -p '/construction/biology/mummer/stage/usr/local/bin' /bin/sh ./libtool --mode=install install -s -m 555 mummer show-coords show-aligns show-snps show-tiling show-diff repeat-match annotate combineMUMs delta-filter nucmer '/construction/biology/mummer/stage/usr/local/bin' libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/mummer /construction/biology/mummer/stage/usr/local/bin/mummer libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/show-coords /construction/biology/mummer/stage/usr/local/bin/show-coords libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/show-aligns /construction/biology/mummer/stage/usr/local/bin/show-aligns libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/show-snps /construction/biology/mummer/stage/usr/local/bin/show-snps libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/show-tiling /construction/biology/mummer/stage/usr/local/bin/show-tiling libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/show-diff /construction/biology/mummer/stage/usr/local/bin/show-diff libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/repeat-match /construction/biology/mummer/stage/usr/local/bin/repeat-match libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/annotate /construction/biology/mummer/stage/usr/local/bin/annotate libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/combineMUMs /construction/biology/mummer/stage/usr/local/bin/combineMUMs libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/delta-filter /construction/biology/mummer/stage/usr/local/bin/delta-filter libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/nucmer /construction/biology/mummer/stage/usr/local/bin/nucmer /bin/mkdir -p '/construction/biology/mummer/stage/usr/local/bin' install -m 555 .libs/mummerplot .libs/dnadiff .libs/promer .libs/exact-tandems '/construction/biology/mummer/stage/usr/local/bin' /bin/mkdir -p '/construction/biology/mummer/stage/usr/local/libexec/mummer' /bin/sh ./libtool --mode=install install -s -m 555 mgaps postnuc prepro postpro '/construction/biology/mummer/stage/usr/local/libexec/mummer' libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/mgaps /construction/biology/mummer/stage/usr/local/libexec/mummer/mgaps libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/postnuc /construction/biology/mummer/stage/usr/local/libexec/mummer/postnuc libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/prepro /construction/biology/mummer/stage/usr/local/libexec/mummer/prepro libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -s .libs/postpro /construction/biology/mummer/stage/usr/local/libexec/mummer/postpro /bin/mkdir -p '/construction/biology/mummer/stage/usr/local/include/mummer-4.0.0beta2' /bin/mkdir -p '/construction/biology/mummer/stage/usr/local/include/mummer-4.0.0beta2/include/jellyfish' install -m 0644 include/jellyfish/circular_buffer.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/cpp_array.hpp include/jellyfish/divisor.hpp include/jellyfish/stream_manager.hpp include/jellyfish/whole_sequence_parser.hpp '/construction/biology/mummer/stage/usr/local/include/mummer-4.0.0beta2/include/jellyfish' /bin/mkdir -p '/construction/biology/mummer/stage/usr/local/include/mummer-4.0.0beta2/include/mummer' install -m 0644 include/mummer/sparseSA.hpp include/mummer/fasta.hpp include/mummer/postnuc.hh include/mummer/translate.hh include/mummer/sw_align.hh include/mummer/tigrinc.hh include/mummer/nucmer.hpp include/mummer/mgaps.hh include/mummer/delta.hh include/mummer/sw_alignscore.hh include/mummer/sparseSA_imp.hpp include/mummer/timer.hpp include/mummer/48bit_index.hpp include/mummer/48bit_iterator.hpp include/mummer/const_iterator_traits.hpp include/mummer/dset.hpp include/mummer/openmp_qsort.hpp include/mummer/redirect_to_pager.hpp '/construction/biology/mummer/stage/usr/local/include/mummer-4.0.0beta2/include/mummer' /bin/mkdir -p '/construction/biology/mummer/stage/usr/local/include/mummer-4.0.0beta2/include/mt_skip_list' install -m 0644 include/mt_skip_list/common.hpp include/mt_skip_list/set.hpp '/construction/biology/mummer/stage/usr/local/include/mummer-4.0.0beta2/include/mt_skip_list' /bin/mkdir -p '/construction/biology/mummer/stage/usr/local/include/mummer-4.0.0beta2/include/thread_pipe' install -m 0644 include/thread_pipe/circular_buffer.hpp include/thread_pipe/cooperative_pool2.hpp include/thread_pipe/divisor.hpp include/thread_pipe/traits.hpp '/construction/biology/mummer/stage/usr/local/include/mummer-4.0.0beta2/include/thread_pipe' /bin/mkdir -p '/construction/biology/mummer/stage/usr/local/include/mummer-4.0.0beta2/include/compactsufsort' install -m 0644 include/compactsufsort/compactsufsort.hpp include/compactsufsort/const_iterator_traits.hpp include/compactsufsort/said_traits.hpp include/compactsufsort/trsort_imp.hpp include/compactsufsort/compactsufsort_imp.hpp include/compactsufsort/divsufsort_private.h include/compactsufsort/sssort_imp.hpp '/construction/biology/mummer/stage/usr/local/include/mummer-4.0.0beta2/include/compactsufsort' /bin/mkdir -p '/construction/biology/mummer/stage/usr/local/include/mummer-4.0.0beta2/include' install -m 0644 include/thread_pipe.hpp '/construction/biology/mummer/stage/usr/local/include/mummer-4.0.0beta2/include' /bin/mkdir -p '/construction/biology/mummer/stage/usr/local/lib/pkgconfig' install -m 0644 mummer.pc '/construction/biology/mummer/stage/usr/local/lib/pkgconfig' /bin/mkdir -p '/construction/biology/mummer/stage/usr/local/lib/mummer' install -m 555 scripts/Foundation.pm scripts/tandem-repeat.awk '/construction/biology/mummer/stage/usr/local/lib/mummer' gmake[3]: Leaving directory '/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5' gmake[2]: Leaving directory '/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5' gmake[1]: Leaving directory '/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: 'lib/libumdmummer.so.0.0.0' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD} Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- 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 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for mummer-4.0.0.b2.2_3 file sizes/checksums [63]: 0% file sizes/checksums [63]: 100% packing files [63]: 0% packing files [63]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:02 TOTAL TIME 00:00:55