=>> Building biology/mummer build started at Wed Mar 11 04:51:19 EDT 2026 port directory: /usr/ports/biology/mummer package name: mummer-4.0.1 building for: FreeBSD pkg.DaveG.ca 14.4-RELEASE FreeBSD 14.4-RELEASE 1404000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1061 Feb 9 2025 /usr/ports/biology/mummer/Makefile Ports top last git commit: 26b198eb3ee3 Ports top unclean checkout: no Port dir last git commit: 297ffe8d7f3c Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1404000 Job Id: 10 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1404000 UNAME_v=FreeBSD 14.4-RELEASE 1404000 UNAME_r=14.4-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/10/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_4_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --disable-static --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/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=/wrkdirs/usr/ports/biology/mummer/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mummer/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/mummer/work/.cache HOME=/wrkdirs/usr/ports/biology/mummer/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mummer/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/mummer/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.72 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mummer/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mummer/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/mummer/work/.cache HOME=/wrkdirs/usr/ports/biology/mummer/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mummer/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/mummer/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DEFAULT_AUTOCONF=2.72 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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" --End MAKE_ENV-- --PLIST_SUB-- OSREL=14.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.0 PERL_VER=5.42 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/5.42 DOCSDIR="share/doc/mummer" EXAMPLESDIR="share/examples/mummer" DATADIR="share/mummer" WWWDIR="www/mummer" ETCDIR="etc/mummer" --End PLIST_SUB-- --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 --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> mummer-4.0.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> mummer-4.0.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mummer-4.0.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by mummer-4.0.1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by mummer-4.0.1 for building => SHA256 Checksum OK for mummer4-mummer-v4.0.1_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by mummer-4.0.1 for building ===> Extracting for mummer-4.0.1 => SHA256 Checksum OK for mummer4-mummer-v4.0.1_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for mummer-4.0.1 ===> Applying FreeBSD patches for mummer-4.0.1 from /usr/ports/biology/mummer/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> mummer-4.0.1 depends on executable: yaggo - not found ===> Installing existing package /packages/All/yaggo-1.5.11_1.pkg [pkg.DaveG.ca] Installing yaggo-1.5.11_1... [pkg.DaveG.ca] `-- Installing ruby-3.3.10,1... [pkg.DaveG.ca] | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | `-- Installing libunwind-20250904... [pkg.DaveG.ca] | `-- Extracting libunwind-20250904: .......... done [pkg.DaveG.ca] | `-- Installing libyaml-0.2.5... [pkg.DaveG.ca] | `-- Extracting libyaml-0.2.5: ...... done [pkg.DaveG.ca] `-- Extracting ruby-3.3.10,1: .......... done [pkg.DaveG.ca] Extracting yaggo-1.5.11_1: ... done ===== Message from ruby-3.3.10,1: -- Some of the standard commands and libraries are provided as separate ports for ease of upgrading: devel/ruby-gems: gem - RubyGems package manager devel/rubygem-debug: debug - Debugging functionality for Ruby devel/rubygem-erb: erb - Templating system for Ruby devel/rubygem-irb: irb - Interactive Ruby devel/rubygem-minitest: minitest - Complete suite of testing facilities devel/rubygem-power_assert: power_assert - Power Assert for Ruby devel/rubygem-racc: racc - LALR(1) parser generator for Ruby devel/rubygem-rake: rake - Ruby Make devel/rubygem-rbs: rbs - Language for type signatures for Ruby and standard library definitions devel/rubygem-rdoc: rdoc - Ruby Documentation System devel/rubygem-test-unit: test-unit - Unit testing framework for Ruby devel/rubygem-typeprof: typeprof - Type analysis tool for Ruby code ftp/rubygem-net-ftp: net-ftp - Support for the File Transfer Protocol mail/rubygem-net-imap: net-imap - Ruby client api for Internet Message Access Protocol mail/rubygem-net-pop: net-pop - Ruby client library for POP3 mail/rubygem-net-smtp: net-smtp - Simple Mail Transfer Protocol client library for Ruby math/rubygem-matrix: matrix - Implementation of Matrix and Vector classes math/rubygem-prime: prime - Prime numbers and factorization library sysutils/rubygem-bundler: bundler - Tool that manages gem dependencies for ruby applications textproc/rubygem-rexml: rexml - XML toolkit for Ruby www/rubygem-rss: rss - Family of libraries that support various formats of XML "feeds" Install them as occasion demands. ===> mummer-4.0.1 depends on executable: yaggo - found ===> Returning to build of mummer-4.0.1 ===> mummer-4.0.1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> mummer-4.0.1 depends on package: gmake>=4.4.1 - found ===> Returning to build of mummer-4.0.1 ===> mummer-4.0.1 depends on package: autoconf>=2.72_1 - not found ===> Installing existing package /packages/All/autoconf-2.72_1.pkg [pkg.DaveG.ca] Installing autoconf-2.72_1... [pkg.DaveG.ca] `-- Installing autoconf-switch-20220527... [pkg.DaveG.ca] `-- Extracting autoconf-switch-20220527: ....... done [pkg.DaveG.ca] `-- Installing m4-1.4.20,1... [pkg.DaveG.ca] `-- Extracting m4-1.4.20,1: .......... done [pkg.DaveG.ca] `-- Installing perl5-5.42.0_1... [pkg.DaveG.ca] `-- Extracting perl5-5.42.0_1: .......... done [pkg.DaveG.ca] Extracting autoconf-2.72_1: .......... done ===> mummer-4.0.1 depends on package: autoconf>=2.72_1 - found ===> Returning to build of mummer-4.0.1 ===> mummer-4.0.1 depends on package: automake>=1.18.1 - not found ===> Installing existing package /packages/All/automake-1.18.1.pkg [pkg.DaveG.ca] Installing automake-1.18.1... [pkg.DaveG.ca] Extracting automake-1.18.1: .......... done ===> mummer-4.0.1 depends on package: automake>=1.18.1 - found ===> Returning to build of mummer-4.0.1 ===> mummer-4.0.1 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.5.4_1.pkg [pkg.DaveG.ca] Installing libtool-2.5.4_1... [pkg.DaveG.ca] Extracting libtool-2.5.4_1: .......... done ===> mummer-4.0.1 depends on executable: libtoolize - found ===> Returning to build of mummer-4.0.1 ===> mummer-4.0.1 depends on package: perl5>=5.42.r<5.43 - found ===> mummer-4.0.1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> mummer-4.0.1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of mummer-4.0.1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for mummer-4.0.1 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 /usr/ports/Templates/config.site checking build system type... amd64-portbld-freebsd14.4 checking host system type... amd64-portbld-freebsd14.4 checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking whether /usr/local/bin/gmake supports nested variables... yes checking xargs -n works... yes checking whether UID '0' is supported by ustar format... yes checking whether GID '0' is supported by ustar format... yes checking how to create a ustar tar archive... (cached) /usr/bin/tar checking how to print strings... printf checking whether /usr/local/bin/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 the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... 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 checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 524288 checking how to convert amd64-portbld-freebsd14.4 file names to amd64-portbld-freebsd14.4 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd14.4 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file 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 ranlib... ranlib checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking command to parse /usr/bin/nm 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 for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd14.4 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 the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed 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... freebsd14.4 ld.so checking how to hardcode library paths into programs... immediate checking for gcc... (cached) cc checking whether the compiler supports GNU C... (cached) yes checking whether cc accepts -g... (cached) yes checking for cc option to enable C11 features... (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 samtools... 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/perl5/5.42/mach/CORE checking for Perl extension target directory... /usr/local/lib/perl5/site_perl/mach/5.42 checking for Perl extensions C preprocessor flags... -DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -DNO_POSIX_2008_LOCALE -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib/perl5/5.42/mach/CORE -lperl -L/usr/local/lib -fstack-protector-strong configure: compiling with flags: CXXFLAGS=-O2 -pipe -fstack-protector-strong -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 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for mummer-4.0.1 /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/one_cmdline.hpp tests/ufasta_src/one_cmdline.yaggo /usr/local/bin/yaggo -o tests/ufasta_src/sizes_cmdline.hpp tests/ufasta_src/sizes_cmdline.yaggo /usr/local/bin/yaggo -o tests/ufasta_src/head_cmdline.hpp tests/ufasta_src/head_cmdline.yaggo /usr/local/bin/yaggo -o tests/ufasta_src/tail_cmdline.hpp tests/ufasta_src/tail_cmdline.yaggo /usr/local/bin/yaggo -o tests/ufasta_src/rc_cmdline.hpp tests/ufasta_src/rc_cmdline.yaggo /usr/local/bin/yaggo -o tests/ufasta_src/n50_cmdline.hpp tests/ufasta_src/n50_cmdline.yaggo /usr/local/bin/yaggo -o tests/ufasta_src/extract_cmdline.hpp tests/ufasta_src/extract_cmdline.yaggo /usr/local/bin/yaggo -o tests/ufasta_src/format_cmdline.hpp tests/ufasta_src/format_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/ufasta_src/dsort_cmdline.hpp tests/ufasta_src/dsort_cmdline.yaggo /usr/local/bin/yaggo -o tests/ufasta_src/split_cmdline.hpp tests/ufasta_src/split_cmdline.yaggo /usr/local/bin/yaggo -o tests/ufasta_src/rsort_cmdline.hpp tests/ufasta_src/rsort_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 /usr/local/bin/gmake all-am gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1' sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1,g' -e 's,[@]LIB_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1,g' -e 's,[@]MUMMER[@],mummer,g' -e 's,[@]MGAPS[@],mgaps,g' -e 's,[@]PRENUC[@],prenuc,g' -e 's,[@]POSTNUC[@],postnuc,g' -e 's,[@]PREPRO[@],prepro,g' -e 's,[@]POSTPRO[@],postpro,g' -e 's,[@]SHOWCOORDS[@],show-coords,g' -e 's,[@]SHOWDIFF[@],show-diff,g' -e 's,[@]SHOWSNPS[@],show-snps,g' -e 's,[@]NUCMER[@],nucmer,g' -e 's,[@]DELTAFILTER[@],delta-filter,g' -e 's,[@]REPEATMATCH[@],repeat-match,g' < scripts/mummerplot.pl > mummerplot && chmod a+x mummerplot sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1,g' -e 's,[@]LIB_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1,g' -e 's,[@]MUMMER[@],mummer,g' -e 's,[@]MGAPS[@],mgaps,g' -e 's,[@]PRENUC[@],prenuc,g' -e 's,[@]POSTNUC[@],postnuc,g' -e 's,[@]PREPRO[@],prepro,g' -e 's,[@]POSTPRO[@],postpro,g' -e 's,[@]SHOWCOORDS[@],show-coords,g' -e 's,[@]SHOWDIFF[@],show-diff,g' -e 's,[@]SHOWSNPS[@],show-snps,g' -e 's,[@]NUCMER[@],nucmer,g' -e 's,[@]DELTAFILTER[@],delta-filter,g' -e 's,[@]REPEATMATCH[@],repeat-match,g' < scripts/dnadiff.pl > dnadiff && chmod a+x dnadiff sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1,g' -e 's,[@]LIB_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1,g' -e 's,[@]MUMMER[@],mummer,g' -e 's,[@]MGAPS[@],mgaps,g' -e 's,[@]PRENUC[@],prenuc,g' -e 's,[@]POSTNUC[@],postnuc,g' -e 's,[@]PREPRO[@],prepro,g' -e 's,[@]POSTPRO[@],postpro,g' -e 's,[@]SHOWCOORDS[@],show-coords,g' -e 's,[@]SHOWDIFF[@],show-diff,g' -e 's,[@]SHOWSNPS[@],show-snps,g' -e 's,[@]NUCMER[@],nucmer,g' -e 's,[@]DELTAFILTER[@],delta-filter,g' -e 's,[@]REPEATMATCH[@],repeat-match,g' < scripts/promer.pl > promer && chmod a+x promer sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1,g' -e 's,[@]LIB_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1,g' -e 's,[@]MUMMER[@],mummer,g' -e 's,[@]MGAPS[@],mgaps,g' -e 's,[@]PRENUC[@],prenuc,g' -e 's,[@]POSTNUC[@],postnuc,g' -e 's,[@]PREPRO[@],prepro,g' -e 's,[@]POSTPRO[@],postpro,g' -e 's,[@]SHOWCOORDS[@],show-coords,g' -e 's,[@]SHOWDIFF[@],show-diff,g' -e 's,[@]SHOWSNPS[@],show-snps,g' -e 's,[@]NUCMER[@],nucmer,g' -e 's,[@]DELTAFILTER[@],delta-filter,g' -e 's,[@]REPEATMATCH[@],repeat-match,g' < scripts/delta2vcf.pl > delta2vcf && chmod a+x delta2vcf sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1,g' -e 's,[@]LIB_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1,g' -e 's,[@]MUMMER[@],mummer,g' -e 's,[@]MGAPS[@],mgaps,g' -e 's,[@]PRENUC[@],prenuc,g' -e 's,[@]POSTNUC[@],postnuc,g' -e 's,[@]PREPRO[@],prepro,g' -e 's,[@]POSTPRO[@],postpro,g' -e 's,[@]SHOWCOORDS[@],show-coords,g' -e 's,[@]SHOWDIFF[@],show-diff,g' -e 's,[@]SHOWSNPS[@],show-snps,g' -e 's,[@]NUCMER[@],nucmer,g' -e 's,[@]DELTAFILTER[@],delta-filter,g' -e 's,[@]REPEATMATCH[@],repeat-match,g' < scripts/nucmer_ori.pl > nucmer_ori && chmod a+x nucmer_ori sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1,g' -e 's,[@]LIB_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1,g' -e 's,[@]MUMMER[@],mummer,g' -e 's,[@]MGAPS[@],mgaps,g' -e 's,[@]PRENUC[@],prenuc,g' -e 's,[@]POSTNUC[@],postnuc,g' -e 's,[@]PREPRO[@],prepro,g' -e 's,[@]POSTPRO[@],postpro,g' -e 's,[@]SHOWCOORDS[@],show-coords,g' -e 's,[@]SHOWDIFF[@],show-diff,g' -e 's,[@]SHOWSNPS[@],show-snps,g' -e 's,[@]NUCMER[@],nucmer,g' -e 's,[@]DELTAFILTER[@],delta-filter,g' -e 's,[@]REPEATMATCH[@],repeat-match,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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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 $depbase.Plo depbase=`echo src/tigr/mgaps.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -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 $depbase.Plo depbase=`echo src/tigr/postnuc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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 $depbase.Plo depbase=`echo src/tigr/tigrinc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -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 $depbase.Plo depbase=`echo src/umd/nucmer.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ./libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -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 $depbase.Plo depbase=`echo src/tigr/show-coords.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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 $depbase.Po depbase=`echo src/tigr/prenuc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/tigr/prenuc.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/prenuc.o src/tigr/prenuc.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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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 libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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 libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -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 libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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 /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -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/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 -lc++ -lm -lc -lgcc -lgcc_s /usr/lib/crtendS.o /usr/lib/crtn.o -fopenmp -O2 -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -o repeat-match src/tigr/repeat-match.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -o annotate src/tigr/annotate.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -o combineMUMs src/tigr/combineMUMs.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -o delta-filter src/tigr/delta-filter.o src/tigr/delta.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -o mgaps src/tigr/mgaps_main.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -o prenuc src/tigr/prenuc.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -o postnuc src/tigr/postnuc_main.o libumdmummer.la /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -o postpro src/tigr/postpro.o src/tigr/translate.o libumdmummer.la libtool: link: c++ -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/annotate src/tigr/annotate.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib libtool: link: c++ -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -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 libtool: link: c++ -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/prenuc src/tigr/prenuc.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib libtool: link: c++ -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -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++17 -fopenmp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -o nucmer src/umd/nucmer_main.o libumdmummer.la libtool: link: c++ -std=c++17 -fopenmp -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -o .libs/nucmer src/umd/nucmer_main.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> mummer-4.0.1 depends on package: perl5>=5.42.r<5.43 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for mummer-4.0.1 ===> Generating temporary packing list if test -z 'strip'; then \ /usr/local/bin/gmake INSTALL_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ install; \ else \ /usr/local/bin/gmake INSTALL_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ "INSTALL_PROGRAM_ENV=STRIPPROG='strip'" install; \ fi gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1' /usr/local/bin/gmake install-am gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/lib' /bin/sh ./libtool --mode=install /usr/bin/install -c -s libumdmummer.la '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libumdmummer.so.0.0.0 /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/lib/libumdmummer.so.0.0.0 libtool: install: strip --strip-unneeded /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/lib/libumdmummer.so.0.0.0 libtool: install: (cd /wrkdirs/usr/ports/biology/mummer/work/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 /wrkdirs/usr/ports/biology/mummer/work/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 /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/lib/libumdmummer.la libtool: warning: remember to run 'libtool --finish /usr/local/lib' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin' STRIPPROG='strip' /bin/sh ./libtool --mode=install /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s mummer show-coords show-aligns show-snps show-tiling show-diff repeat-match annotate combineMUMs delta-filter nucmer '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin' libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/mummer /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin/mummer libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/show-coords /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin/show-coords libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/show-aligns /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin/show-aligns libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/show-snps /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin/show-snps libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/show-tiling /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin/show-tiling libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/show-diff /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin/show-diff libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/repeat-match /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin/repeat-match libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/annotate /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin/annotate libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/combineMUMs /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin/combineMUMs libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/delta-filter /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin/delta-filter libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/nucmer /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin/nucmer /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin' install -m 555 .libs/mummerplot .libs/dnadiff .libs/promer .libs/exact-tandems '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/libexec/mummer' STRIPPROG='strip' /bin/sh ./libtool --mode=install /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s mgaps prenuc postnuc prepro postpro '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/libexec/mummer' libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/mgaps /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/libexec/mummer/mgaps libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/prenuc /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/libexec/mummer/prenuc libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/postnuc /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/libexec/mummer/postnuc libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/prepro /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/libexec/mummer/prepro libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1/install-sh -c -s .libs/postpro /wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/libexec/mummer/postpro /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/libexec/mummer' install -m 555 .libs/nucmer_ori '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/libexec/mummer' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.1' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.1/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 '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.1/include/jellyfish' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.1/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 '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.1/include/mummer' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.1/include/mt_skip_list' install -m 0644 include/mt_skip_list/common.hpp include/mt_skip_list/set.hpp '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.1/include/mt_skip_list' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.1/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 '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.1/include/thread_pipe' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.1/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 '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.1/include/compactsufsort' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.1/include' install -m 0644 include/thread_pipe.hpp '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.1/include' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/lib/pkgconfig' install -m 0644 mummer.pc '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/lib/pkgconfig' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/lib/mummer' install -m 0644 scripts/Foundation.pm scripts/tandem-repeat.awk '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/lib/mummer' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.1' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-03-11T08:51:19+0000' 'PKG_NOTE_ports_top_git_hash=26b198eb3ee3' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=297ffe8d7f3c' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for mummer-4.0.1 ===> Building mummer-4.0.1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for mummer-4.0.1 build of biology/mummer | mummer-4.0.1 ended at Wed Mar 11 04:52:07 EDT 2026 build time: 00:00:50