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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/beefy24/data/main-amd64-default/pc15851b5d6fc_s7dc4284615/logs/mummer-4.0.1.log Build URL: https://pkg-status.freebsd.org/beefy24/build.html?mastername=main-amd64-default&build=pc15851b5d6fc_s7dc4284615 Log: =>> Building biology/mummer build started at Sat Aug 29 03:15:57 UTC 2026 port directory: /usr/ports/biology/mummer package name: mummer-4.0.1 building for: FreeBSD main-amd64-default-job-03 16.0-CURRENT FreeBSD 16.0-CURRENT 1600021 amd64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 1061 Sep 30 2025 /usr/ports/biology/mummer/Makefile Ports top last git commit: c15851b5d6fc3781f592602edc35589c21774938 Ports top unclean checkout: no Port dir last git commit: b64b73fd938d5b2788547d16ed6a76493acc9142 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.8-2-g2e891d4a Host OSVERSION: 1600019 Jail OSVERSION: 1600021 Job Id: 03 !!! Jail is newer than host. (Jail: 1600021, Host: 1600019) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1600021 UNAME_v=FreeBSD 16.0-CURRENT 1600021 UNAME_r=16.0-CURRENT 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=3.4.8-2-g2e891d4a MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/main-amd64-default/03/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.8-2-g2e891d4a 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-- [email protected] --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=2.73 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=2.73 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="insta ll -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=16.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.3 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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### 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 (kbytes, -y) unlimited virtual machines (-V) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License ART10 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== 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-2.8.4.pkg [main-amd64-default-job-03] Installing pkg-2.8.4... [main-amd64-default-job-03] Extracting pkg-2.8.4: .......... done ===> mummer-4.0.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mummer-4.0.1 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License ART10 accepted by the user ===> Fetching all distfiles required by mummer-4.0.1 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License ART10 accepted by the user ===> Fetching all distfiles required by mummer-4.0.1 for building => SHA256 Checksum OK for mummer4-mummer-v4.0.1_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License ART10 accepted by the user ===> 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. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== 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 =========================================================================== =======================<phase: build-depends >============================ ===== 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 [main-amd64-default-job-03] Installing yaggo-1.5.11_1... [main-amd64-default-job-03] `-- Installing ruby-3.4.9_2,1... [main-amd64-default-job-03] | `-- Installing libffi-3.8.0... [main-amd64-default-job-03] | | `-- Installing indexinfo-0.3.1_1... [main-amd64-default-job-03] | | `-- Extracting indexinfo-0.3.1_1: .... done [main-amd64-default-job-03] | `-- Extracting libffi-3.8.0: .......... done [main-amd64-default-job-03] | `-- Installing libunwind-20250904... [main-amd64-default-job-03] | `-- Extracting libunwind-20250904: .......... done [main-amd64-default-job-03] | `-- Installing libyaml-0.2.5... [main-amd64-default-job-03] | `-- Extracting libyaml-0.2.5: ......... done [main-amd64-default-job-03] `-- Extracting ruby-3.4.9_2,1: .......... done [main-amd64-default-job-03] Extracting yaggo-1.5.11_1: ...... done <snip> 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 [main-amd64-default-job-03] Installing gmake-4.4.1... [main-amd64-default-job-03] `-- Installing gettext-runtime-1.0_1... [main-amd64-default-job-03] `-- Extracting gettext-runtime-1.0_1: .......... done [main-amd64-default-job-03] 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>=2.73 - not found ===> Installing existing package /packages/All/autoconf-2.73.pkg [main-amd64-default-job-03] Installing autoconf-2.73... [main-amd64-default-job-03] `-- Installing autoconf-switch-20220527... [main-amd64-default-job-03] `-- Extracting autoconf-switch-20220527: .......... done [main-amd64-default-job-03] `-- Installing m4-1.4.21,1... [main-amd64-default-job-03] `-- Extracting m4-1.4.21,1: .......... done [main-amd64-default-job-03] `-- Installing perl5-5.42.3... [main-amd64-default-job-03] `-- Extracting perl5-5.42.3: .......... done [main-amd64-default-job-03] Extracting autoconf-2.73: .......... done ===> mummer-4.0.1 depends on package: autoconf>=2.73 - 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 [main-amd64-default-job-03] Installing automake-1.18.1... [main-amd64-default-job-03] 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 [main-amd64-default-job-03] Installing libtool-2.5.4_1... [main-amd64-default-job-03] 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 =========================================================================== =======================<phase: lib-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: configure >============================ ===== 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-freebsd16.0 checking host system type... amd64-portbld-freebsd16.0 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 C23 features... unsupported 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 -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) 524288 checking how to convert amd64-portbld-freebsd16.0 file names to amd64-portbld-freebsd16.0 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd16.0 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... @ checking for strip... strip 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 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... freebsd16.0 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 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... freebsd16.0 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 C23 features... (cached) unsupported 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 =========================================================================== =======================<phase: build >============================ ===== 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 ld-elf.so.1: Shared object "libruby34.so.34" not found, required by "ruby" gmake: *** [Makefile:3335: src/umd/nucmer_cmdline.hpp] Error 1 gmake: *** Waiting for unfinished jobs.... ld-elf.so.1: Shared object "libruby34.so.34" not found, required by "ruby" gmake: *** [Makefile:3335: tests/generate_sequences_cmdline.hpp] Error 1 ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped making "build" in /usr/ports/biology/mummer
