=> Building biology/mummer Started : Sunday, 7 JUL 2019 at 04:25:27 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/mummer XDG_CONFIG_HOME=/construction/biology/mummer HOME=/construction/biology/mummer TMPDIR="/tmp" PATH=/construction/biology/mummer/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --disable-static --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/mummer XDG_CONFIG_HOME=/construction/biology/mummer HOME=/construction/biology/mummer TMPDIR="/tmp" PATH=/construction/biology/mummer/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/mummer/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.2 PERL_VER=5.28 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.28 PROFILE="@comment " DOCSDIR="share/doc/mummer" EXAMPLESDIR="share/examples/mummer" DATADIR="share/mummer" WWWDIR="www/mummer" ETCDIR="etc/mummer" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mummer DOCSDIR=/usr/local/share/doc/mummer EXAMPLESDIR=/usr/local/share/examples/mummer WWWDIR=/usr/local/www/mummer ETCDIR=/usr/local/etc/mummer -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.4 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License ART10 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> mummer-4.0.0.b2.2_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> mummer-4.0.0.b2.2_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mummer-4.0.0.b2.2_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License ART10 accepted by the user ===> Fetching all distfiles required by mummer-4.0.0.b2.2_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License ART10 accepted by the user ===> Fetching all distfiles required by mummer-4.0.0.b2.2_1 for building => SHA256 Checksum OK for mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License ART10 accepted by the user ===> Fetching all distfiles required by mummer-4.0.0.b2.2_1 for building ===> Extracting for mummer-4.0.0.b2.2_1 => SHA256 Checksum OK for mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for mummer-4.0.0.b2.2_1 ===> Applying ports patches for mummer-4.0.0.b2.2_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> mummer-4.0.0.b2.2_1 depends on executable: yaggo - not found ===> Installing existing package /packages/All/yaggo-1.5.9.txz Installing yaggo-1.5.9... `-- Installing ruby-2.5.5_2,1... | `-- Installing libedit-3.1.20190324,1... | | `-- Installing ncurses-6.1.20190525... | | `-- Extracting ncurses-6.1.20190525: .......... done | `-- Extracting libedit-3.1.20190324,1: .......... done | `-- Installing libffi-3.2.1_3... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | `-- Extracting libffi-3.2.1_3: .......... done | `-- Installing libressl-2.9.2... | `-- Extracting libressl-2.9.2: .......... done | `-- Installing libyaml-0.2.2... | `-- Extracting libyaml-0.2.2: ......... done `-- Extracting ruby-2.5.5_2,1: .......... done Extracting yaggo-1.5.9: ...... done Message from ruby-2.5.5_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-rake: rake - Ruby Make 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. ==== ===> mummer-4.0.0.b2.2_1 depends on executable: yaggo - found ===> Returning to build of mummer-4.0.0.b2.2_1 ===> mummer-4.0.0.b2.2_1 depends on package: autoconf>=2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69_2.txz Installing autoconf-2.69_2... `-- Installing autoconf-wrapper-20131203... `-- Extracting autoconf-wrapper-20131203: .......... done `-- Installing m4-1.4.18_1,1... `-- Extracting m4-1.4.18_1,1: .......... done `-- Installing perl5-5.28.2... `-- Extracting perl5-5.28.2: .......... done Extracting autoconf-2.69_2: .......... done Message from perl5-5.28.2: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> mummer-4.0.0.b2.2_1 depends on package: autoconf>=2.69 - found ===> Returning to build of mummer-4.0.0.b2.2_1 ===> mummer-4.0.0.b2.2_1 depends on package: automake>=1.16.1 - not found ===> Installing existing package /packages/All/automake-1.16.1_1.txz Installing automake-1.16.1_1... Extracting automake-1.16.1_1: .......... done ===> mummer-4.0.0.b2.2_1 depends on package: automake>=1.16.1 - found ===> Returning to build of mummer-4.0.0.b2.2_1 ===> mummer-4.0.0.b2.2_1 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.4.6_1.txz Installing libtool-2.4.6_1... Extracting libtool-2.4.6_1: .......... done ===> mummer-4.0.0.b2.2_1 depends on executable: libtoolize - found ===> Returning to build of mummer-4.0.0.b2.2_1 ===> mummer-4.0.0.b2.2_1 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... `-- Installing gettext-runtime-0.20.1... `-- Extracting gettext-runtime-0.20.1: .......... done Extracting gmake-4.2.1_3: .......... done ===> mummer-4.0.0.b2.2_1 depends on executable: gmake - found ===> Returning to build of mummer-4.0.0.b2.2_1 ===> mummer-4.0.0.b2.2_1 depends on package: perl5>=5.28.r1<5.29 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for mummer-4.0.0.b2.2_1 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-dragonfly5.4 checking host system type... x86_64-portbld-dragonfly5.4 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-dragonfly5.4 file names to x86_64-portbld-dragonfly5.4 format... func_convert_file_noop checking how to convert x86_64-portbld-dragonfly5.4 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... dragonfly5.4 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... dragonfly5.4 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/perl5/5.28/mach/CORE checking for Perl extension target directory... /usr/local/lib/perl5/site_perl/mach/5.28 checking for Perl extensions C preprocessor flags... -DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib/perl5/5.28/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 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for mummer-4.0.0.b2.2_1 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' 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 $depbase.Po depbase=`echo src/umd/nucmer_main.o | sed 's|[^/]*$|.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 $depbase.Po sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]GNUPLOT_EXE[@],false,g' < scripts/mummerplot.pl > mummerplot && chmod a+x mummerplot sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]GNUPLOT_EXE[@],false,g' < scripts/dnadiff.pl > dnadiff && chmod a+x dnadiff sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]GNUPLOT_EXE[@],false,g' < scripts/promer.pl > promer && chmod a+x promer sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/construction/biology/mummer/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]GNUPLOT_EXE[@],false,g' < scripts/exact-tandems.sh > exact-tandems && chmod a+x exact-tandems depbase=`echo src/essaMEM/fasta.o | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/essaMEM/sparseSA.lo -MD -MP -MF src/essaMEM/.deps/sparseSA.Tpo -c src/essaMEM/sparseSA.cpp -fPIC -DPIC -o src/essaMEM/.libs/sparseSA.o depbase=`echo src/essaMEM/sssort_compact.lo | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/essaMEM/sssort_compact.lo -MD -MP -MF src/essaMEM/.deps/sssort_compact.Tpo -c src/essaMEM/sssort_compact.cc -fPIC -DPIC -o src/essaMEM/.libs/sssort_compact.o depbase=`echo src/tigr/mgaps.lo | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/postnuc.lo -MD -MP -MF src/tigr/.deps/postnuc.Tpo -c src/tigr/postnuc.cc -fPIC -DPIC -o src/tigr/.libs/postnuc.o depbase=`echo src/tigr/sw_align.lo | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/sw_align.lo -MD -MP -MF src/tigr/.deps/sw_align.Tpo -c src/tigr/sw_align.cc -fPIC -DPIC -o src/tigr/.libs/sw_align.o depbase=`echo src/tigr/tigrinc.lo | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -pipe -O2 -fno-strict-aliasing -MT src/tigr/tigrinc.lo -MD -MP -MF src/tigr/.deps/tigrinc.Tpo -c src/tigr/tigrinc.cc -fPIC -DPIC -o src/tigr/.libs/tigrinc.o depbase=`echo src/umd/nucmer.lo | sed 's|[^/]*$|.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 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 /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 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 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/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/show-tiling src/tigr/show-tiling.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 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 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-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 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/repeat-match src/tigr/repeat-match.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 /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/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 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/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/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/mgaps src/tigr/mgaps_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/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 prepro src/tigr/prepro.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 postpro src/tigr/postpro.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/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 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' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> mummer-4.0.0.b2.2_1 depends on package: perl5>=5.28.r1<5.29 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for mummer-4.0.0.b2.2_1 ===> 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) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for mummer-4.0.0.b2.2_1 file sizes/checksums [66]: . done packing files [66]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:26:37 UTC Duration: 00:01:10