=>> Building biology/mummer build started at Tue Apr 2 13:17:14 BST 2024 port directory: /usr/ports/biology/mummer package name: mummer-4.0.0.b2.2_3 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 778 Nov 6 13:35 /usr/ports/biology/mummer/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 06df180a9e Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 13 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/13/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 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=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=/ccache/libexec/ccache:/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 CCACHE_DIR="/root/.ccache" 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=/ccache/libexec/ccache:/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=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.3 PERL_VER=5.36 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/5.36 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 FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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 --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-4.0.0.b2.2_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> mummer-4.0.0.b2.2_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mummer-4.0.0.b2.2_3 =========================================================================== =================================================== ===== 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-4.0.0.b2.2_3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by mummer-4.0.0.b2.2_3 for building => SHA256 Checksum OK for mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz. =========================================================================== =================================================== ===== 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-4.0.0.b2.2_3 for building ===> Extracting for mummer-4.0.0.b2.2_3 => SHA256 Checksum OK for mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz. =========================================================================== =================================================== ===== 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-4.0.0.b2.2_3 ===> Applying FreeBSD patches for mummer-4.0.0.b2.2_3 from /usr/ports/biology/mummer/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> mummer-4.0.0.b2.2_3 depends on executable: yaggo - not found ===> Installing existing package /packages/All/yaggo-1.5.11_1.pkg [pkg-builder.dan.net.uk] Installing yaggo-1.5.11_1... [pkg-builder.dan.net.uk] `-- Installing ruby-3.2.3,1... [pkg-builder.dan.net.uk] | `-- Installing libedit-3.1.20230828_1,1... [pkg-builder.dan.net.uk] | `-- Extracting libedit-3.1.20230828_1,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libffi-3.4.4_1... [pkg-builder.dan.net.uk] | | `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] | | `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] | `-- Extracting libffi-3.4.4_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libunwind-20240221... [pkg-builder.dan.net.uk] | `-- Extracting libunwind-20240221: .......... done [pkg-builder.dan.net.uk] | `-- Installing libyaml-0.2.5... [pkg-builder.dan.net.uk] | `-- Extracting libyaml-0.2.5: ...... done [pkg-builder.dan.net.uk] | `-- Installing openssl-3.0.13_1,1... [pkg-builder.dan.net.uk] | `-- Extracting openssl-3.0.13_1,1: .......... done [pkg-builder.dan.net.uk] `-- Extracting ruby-3.2.3,1: .......... done [pkg-builder.dan.net.uk] Extracting yaggo-1.5.11_1: ... done ===== Message from ruby-3.2.3,1: -- 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-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" 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_3 depends on executable: yaggo - found ===> Returning to build of mummer-4.0.0.b2.2_3 ===> mummer-4.0.0.b2.2_3 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg-builder.dan.net.uk] Installing gmake-4.4.1... [pkg-builder.dan.net.uk] `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] Extracting gmake-4.4.1: .......... done ===> mummer-4.0.0.b2.2_3 depends on package: gmake>=4.4.1 - found ===> Returning to build of mummer-4.0.0.b2.2_3 ===> mummer-4.0.0.b2.2_3 depends on package: autoconf>=2.72 - not found ===> Installing existing package /packages/All/autoconf-2.72.pkg [pkg-builder.dan.net.uk] Installing autoconf-2.72... [pkg-builder.dan.net.uk] `-- Installing autoconf-switch-20220527... [pkg-builder.dan.net.uk] `-- Extracting autoconf-switch-20220527: ....... done [pkg-builder.dan.net.uk] `-- Installing m4-1.4.19_1,1... [pkg-builder.dan.net.uk] | `-- Installing libsigsegv-2.14... [pkg-builder.dan.net.uk] | `-- Extracting libsigsegv-2.14: ..... done [pkg-builder.dan.net.uk] `-- Extracting m4-1.4.19_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing perl5-5.36.3_1... [pkg-builder.dan.net.uk] `-- Extracting perl5-5.36.3_1: .......... done [pkg-builder.dan.net.uk] Extracting autoconf-2.72: .......... done ===== Message from libsigsegv-2.14: -- Note that the stackoverflow handling functions of this library need procfs mounted on /proc. ===> mummer-4.0.0.b2.2_3 depends on package: autoconf>=2.72 - found ===> Returning to build of mummer-4.0.0.b2.2_3 ===> mummer-4.0.0.b2.2_3 depends on package: automake>=1.16.5 - not found ===> Installing existing package /packages/All/automake-1.16.5_1.pkg [pkg-builder.dan.net.uk] Installing automake-1.16.5_1... [pkg-builder.dan.net.uk] Extracting automake-1.16.5_1: .......... done ===> mummer-4.0.0.b2.2_3 depends on package: automake>=1.16.5 - found ===> Returning to build of mummer-4.0.0.b2.2_3 ===> mummer-4.0.0.b2.2_3 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.4.7_2.pkg [pkg-builder.dan.net.uk] Installing libtool-2.4.7_2... [pkg-builder.dan.net.uk] Extracting libtool-2.4.7_2: .......... done ===> mummer-4.0.0.b2.2_3 depends on executable: libtoolize - found ===> Returning to build of mummer-4.0.0.b2.2_3 ===> mummer-4.0.0.b2.2_3 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== 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-4.0.0.b2.2_3 libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:8: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:8: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:8: the top level configure.ac:71: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:71: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:71: the top level configure.ac:74: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:74: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:74: the top level configure.ac:77: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:77: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:77: the top level configure.ac:80: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:80: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:80: the top level configure.ac:85: warning: The macro 'AC_HELP_STRING' is obsolete. configure.ac:85: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.ac:85: the top level configure.ac:89: warning: The macro 'SWIG_ENABLE_CXX' is obsolete. configure.ac:89: You should run autoupdate. m4/m4-ax_swig_enable_cxx.m4:48: SWIG_ENABLE_CXX is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... configure.ac:89: the top level 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-freebsd13.2 checking host system type... amd64-portbld-freebsd13.2 checking for a BSD-compatible install... /usr/bin/install -c 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 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 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-freebsd13.2 file names to amd64-portbld-freebsd13.2 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd13.2 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... no 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... no checking for strip... strip checking for ranlib... ranlib 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... freebsd13.2 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... freebsd13.2 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 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/perl5/5.36/mach/CORE checking for Perl extension target directory... /usr/local/lib/perl5/site_perl/mach/5.36 checking for Perl extensions C preprocessor flags... -DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -DUSE_THREAD_SAFE_LOCALE -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib/perl5/5.36/mach/CORE -lperl -L/usr/local/lib -fstack-protector-strong configure: compiling with flags: CXXFLAGS=-std=c++0x -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-4.0.0.b2.2_3 /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[1]: Entering directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5' 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 -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++11 -fopenmp -std=c++0x -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++11 -fopenmp -std=c++0x -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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/essaMEM/sparseSA.lo -MD -MP -MF src/essaMEM/.deps/sparseSA.Tpo -c src/essaMEM/sparseSA.cpp -fPIC -DPIC -o src/essaMEM/.libs/sparseSA.o depbase=`echo src/essaMEM/sssort_compact.lo | sed 's|[^/]*$|.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 -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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/essaMEM/sssort_compact.lo -MD -MP -MF src/essaMEM/.deps/sssort_compact.Tpo -c src/essaMEM/sssort_compact.cc -fPIC -DPIC -o src/essaMEM/.libs/sssort_compact.o depbase=`echo src/tigr/mgaps.lo | sed 's|[^/]*$|.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 -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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/tigr/mgaps.lo -MD -MP -MF src/tigr/.deps/mgaps.Tpo -c src/tigr/mgaps.cc -fPIC -DPIC -o src/tigr/.libs/mgaps.o In file included from src/tigr/mgaps.cc:18: In file included from ./include/mummer/mgaps.hh:6: ./include/mummer/dset.hpp:106:13: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] __asm__ __volatile__ ("pause\n"); ^ ./include/mummer/dset.hpp:102:9: note: previous statement is here if ((value & lock_flag) || (uint32_t) value != id) ^ 1 warning generated. depbase=`echo src/tigr/postnuc.lo | sed 's|[^/]*$|.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 -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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/tigr/postnuc.lo -MD -MP -MF src/tigr/.deps/postnuc.Tpo -c src/tigr/postnuc.cc -fPIC -DPIC -o src/tigr/.libs/postnuc.o depbase=`echo src/tigr/sw_align.lo | sed 's|[^/]*$|.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 -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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/tigr/sw_align.lo -MD -MP -MF src/tigr/.deps/sw_align.Tpo -c src/tigr/sw_align.cc -fPIC -DPIC -o src/tigr/.libs/sw_align.o depbase=`echo src/tigr/tigrinc.lo | sed 's|[^/]*$|.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 -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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/tigr/tigrinc.lo -MD -MP -MF src/tigr/.deps/tigrinc.Tpo -c src/tigr/tigrinc.cc -fPIC -DPIC -o src/tigr/.libs/tigrinc.o depbase=`echo src/umd/nucmer.lo | sed 's|[^/]*$|.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 -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 libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -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 In file included from src/umd/nucmer.cc:6: In file included from ./include/mummer/nucmer.hpp:12: In file included from ./include/mummer/mgaps.hh:6: ./include/mummer/dset.hpp:106:13: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] __asm__ __volatile__ ("pause\n"); ^ ./include/mummer/dset.hpp:102:9: note: previous statement is here if ((value & lock_flag) || (uint32_t) value != id) ^ 1 warning generated. /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -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 -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++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o mummer src/essaMEM/fasta.o src/essaMEM/mummer.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/mummer src/essaMEM/fasta.o src/essaMEM/mummer.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib 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 -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++11 -fopenmp -std=c++0x -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 $depbase.Po /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o show-coords src/tigr/show-coords.o src/tigr/delta.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/show-coords src/tigr/show-coords.o src/tigr/delta.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib depbase=`echo src/tigr/show-aligns.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -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++11 -fopenmp -std=c++0x -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 $depbase.Po /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o show-aligns src/tigr/show-aligns.o src/tigr/delta.o src/tigr/translate.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/show-aligns src/tigr/show-aligns.o src/tigr/delta.o src/tigr/translate.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib depbase=`echo src/tigr/show-snps.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -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 $depbase.Po /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o show-snps src/tigr/show-snps.o src/tigr/delta.o src/tigr/translate.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/show-snps src/tigr/show-snps.o src/tigr/delta.o src/tigr/translate.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib depbase=`echo src/tigr/show-tiling.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -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 $depbase.Po /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o show-tiling src/tigr/show-tiling.o src/tigr/delta.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/show-tiling src/tigr/show-tiling.o src/tigr/delta.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib depbase=`echo src/tigr/show-diff.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include 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src/tigr/repeat-match.o src/tigr/repeat-match.cc &&\ mv -f $depbase.Tpo $depbase.Po src/tigr/repeat-match.cc:273:49: warning: variable 'Offset' set but not used [-Wunused-but-set-variable] int Last_Parent_Depth, Link_Depth, Matched, Offset; ^ 1 warning generated. /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o repeat-match src/tigr/repeat-match.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/repeat-match src/tigr/repeat-match.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib depbase=`echo src/tigr/annotate.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -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 $depbase.Po /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o annotate src/tigr/annotate.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/annotate src/tigr/annotate.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib depbase=`echo src/tigr/combineMUMs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -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 $depbase.Po /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o combineMUMs src/tigr/combineMUMs.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/combineMUMs src/tigr/combineMUMs.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib depbase=`echo src/tigr/delta-filter.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -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 $depbase.Po /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o delta-filter src/tigr/delta-filter.o src/tigr/delta.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/delta-filter src/tigr/delta-filter.o src/tigr/delta.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib depbase=`echo src/umd/nucmer_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -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 $depbase.Po In file included from src/umd/nucmer_main.cc:7: In file included from ./include/mummer/nucmer.hpp:12: In file included from ./include/mummer/mgaps.hh:6: ./include/mummer/dset.hpp:106:13: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] __asm__ __volatile__ ("pause\n"); ^ ./include/mummer/dset.hpp:102:9: note: previous statement is here if ((value & lock_flag) || (uint32_t) value != id) ^ 1 warning generated. /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o nucmer src/umd/nucmer_main.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/nucmer src/umd/nucmer_main.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib depbase=`echo src/tigr/mgaps_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -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 $depbase.Po In file included from src/tigr/mgaps_main.cc:18: In file included from ./include/mummer/mgaps.hh:6: ./include/mummer/dset.hpp:106:13: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] __asm__ __volatile__ ("pause\n"); ^ ./include/mummer/dset.hpp:102:9: note: previous statement is here if ((value & lock_flag) || (uint32_t) value != id) ^ 1 warning generated. /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o mgaps src/tigr/mgaps_main.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/mgaps src/tigr/mgaps_main.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib depbase=`echo src/tigr/postnuc_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -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 $depbase.Po /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o postnuc src/tigr/postnuc_main.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/postnuc src/tigr/postnuc_main.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib depbase=`echo src/tigr/prepro.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -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 $depbase.Po /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o prepro src/tigr/prepro.o src/tigr/translate.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/prepro src/tigr/prepro.o src/tigr/translate.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib depbase=`echo src/tigr/postpro.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -fopenmp -std=c++0x -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 /bin/sh ./libtool --tag=CXX --mode=link c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -lpthread -fstack-protector-strong -o postpro src/tigr/postpro.o src/tigr/translate.o libumdmummer.la libtool: link: c++ -std=c++11 -fopenmp -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -o .libs/postpro src/tigr/postpro.o src/tigr/translate.o ./.libs/libumdmummer.so -lpthread -fopenmp -Wl,-rpath -Wl,/usr/local/lib sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/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[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/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[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/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[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]GNUPLOT_EXE[@],false,g' < scripts/exact-tandems.sh > exact-tandems && chmod a+x exact-tandems gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> mummer-4.0.0.b2.2_3 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for mummer-4.0.0.b2.2_3 ===> Generating temporary packing list gmake install-am gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/lib' /bin/sh ./libtool --mode=install /usr/bin/install -c 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: (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' /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 '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/bin' libtool: warning: 'libumdmummer.la' has not been installed in '/usr/local/lib' libtool: install: install -m 555 -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: install -m 555 -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: install -m 555 -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: install -m 555 -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: install -m 555 -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: install -m 555 -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: install -m 555 -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: install -m 555 -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: install -m 555 -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: install -m 555 -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: install -m 555 -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' /bin/sh ./libtool --mode=install install -s -m 555 mgaps 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: install -m 555 -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: install -m 555 -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: install -m 555 -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: install -m 555 -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/include/mummer-4.0.0beta2' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/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 '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.0beta2/include/jellyfish' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/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 '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.0beta2/include/mummer' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/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 '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.0beta2/include/mt_skip_list' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/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 '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.0beta2/include/thread_pipe' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/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 '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.0beta2/include/compactsufsort' /bin/mkdir -p '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.0beta2/include' install -m 0644 include/thread_pipe.hpp '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/include/mummer-4.0.0beta2/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 555 scripts/Foundation.pm scripts/tandem-repeat.awk '/wrkdirs/usr/ports/biology/mummer/work/stage/usr/local/lib/mummer' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5' ====> 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=2024-04-02T12:17:14+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=06df180a9e' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for mummer-4.0.0.b2.2_3 ===> Building mummer-4.0.0.b2.2_3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for mummer-4.0.0.b2.2_3 build of biology/mummer | mummer-4.0.0.b2.2_3 ended at Tue Apr 2 13:26:54 BST 2024 build time: 00:09:40