=>> Building biology/locarna build started at Fri Apr 5 04:05:23 BST 2024 port directory: /usr/ports/biology/locarna package name: locarna-2.0.0_1 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 1188 Mar 7 22:02 /usr/ports/biology/locarna/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c779176e8a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 07 ---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/07/.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-- --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 PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/locarna/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/locarna/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/locarna/work/.cache HOME=/wrkdirs/usr/ports/biology/locarna/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/locarna/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/locarna/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/locarna/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/locarna/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/locarna/work/.cache HOME=/wrkdirs/usr/ports/biology/locarna/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/locarna/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/locarna/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 -I/usr/local/include/catch2 -std=c++14 " 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/locarna" EXAMPLESDIR="share/examples/locarna" DATADIR="share/locarna" WWWDIR="www/locarna" ETCDIR="etc/locarna" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/locarna DOCSDIR=/usr/local/share/doc/locarna EXAMPLESDIR=/usr/local/share/examples/locarna WWWDIR=/usr/local/www/locarna ETCDIR=/usr/local/etc/locarna --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 ===> locarna-2.0.0_1 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 ===> locarna-2.0.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of locarna-2.0.0_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 locarna-2.0.0_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by locarna-2.0.0_1 for building => SHA256 Checksum OK for locarna-2.0.0.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 locarna-2.0.0_1 for building ===> Extracting for locarna-2.0.0_1 => SHA256 Checksum OK for locarna-2.0.0.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 locarna-2.0.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> locarna-2.0.0_1 depends on file: /usr/local/lib/libRNA.a - not found ===> Installing existing package /packages/All/viennarna-2.6.4_2.pkg [pkg-builder.dan.net.uk] Installing viennarna-2.6.4_2... [pkg-builder.dan.net.uk] `-- Installing gcc13-13.2.0_4... [pkg-builder.dan.net.uk] | `-- Installing binutils-2.40_5,1... [pkg-builder.dan.net.uk] | | `-- Installing gettext-runtime-0.22.3_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 gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing zstd-1.5.5_1... [pkg-builder.dan.net.uk] | | `-- Installing liblz4-1.9.4_1,1... [pkg-builder.dan.net.uk] | | `-- Extracting liblz4-1.9.4_1,1: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting zstd-1.5.5_1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting binutils-2.40_5,1: .......... done [pkg-builder.dan.net.uk] | `-- Installing gmp-6.3.0... [pkg-builder.dan.net.uk] | `-- Extracting gmp-6.3.0: .......... done [pkg-builder.dan.net.uk] | `-- Installing mpc-1.3.1_1... [pkg-builder.dan.net.uk] | | `-- Installing mpfr-4.2.1,1... [pkg-builder.dan.net.uk] | | `-- Extracting mpfr-4.2.1,1: .......... done [pkg-builder.dan.net.uk] | `-- Extracting mpc-1.3.1_1: ...... done [pkg-builder.dan.net.uk] `-- Extracting gcc13-13.2.0_4: .......... done create symlink for gcc13 create symlink for gcc13 (world) create symlink for g++13 create symlink for g++13 (world) create symlink for cpp13 create symlink for cpp13 (world) [pkg-builder.dan.net.uk] `-- Installing gsl-2.7.1_1... [pkg-builder.dan.net.uk] `-- Extracting gsl-2.7.1_1: .......... done [pkg-builder.dan.net.uk] `-- Installing lapack-3.12.0_2... [pkg-builder.dan.net.uk] | `-- Installing blas-3.12.0_1... [pkg-builder.dan.net.uk] | `-- Extracting blas-3.12.0_1: ..... done [pkg-builder.dan.net.uk] `-- Extracting lapack-3.12.0_2: .......... done [pkg-builder.dan.net.uk] `-- Installing libICE-1.1.0_2,1... [pkg-builder.dan.net.uk] `-- Extracting libICE-1.1.0_2,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libX11-1.8.7_1,1... [pkg-builder.dan.net.uk] | `-- Installing libxcb-1.16.1... [pkg-builder.dan.net.uk] | | `-- Installing libXau-1.0.9_1... [pkg-builder.dan.net.uk] | | `-- Extracting libXau-1.0.9_1: .......... done [pkg-builder.dan.net.uk] | | `-- Installing libXdmcp-1.1.5... [pkg-builder.dan.net.uk] | | `-- Installing xorgproto-2023.2... [pkg-builder.dan.net.uk] | | `-- Extracting xorgproto-2023.2: .......... done [pkg-builder.dan.net.uk] | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg-builder.dan.net.uk] | `-- Extracting libxcb-1.16.1: .......... done [pkg-builder.dan.net.uk] `-- Extracting libX11-1.8.7_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing libXext-1.3.6,1... [pkg-builder.dan.net.uk] `-- Extracting libXext-1.3.6,1: .......... 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 viennarna-2.6.4_2: .......... done ===== Message from gcc13-13.2.0_4: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc13 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> locarna-2.0.0_1 depends on file: /usr/local/lib/libRNA.a - found ===> Returning to build of locarna-2.0.0_1 ===> locarna-2.0.0_1 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] Extracting gmake-4.4.1: .......... done ===> locarna-2.0.0_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of locarna-2.0.0_1 ===> locarna-2.0.0_1 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.1.1,1.pkg [pkg-builder.dan.net.uk] Installing pkgconf-2.1.1,1... [pkg-builder.dan.net.uk] Extracting pkgconf-2.1.1,1: .......... done ===> locarna-2.0.0_1 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of locarna-2.0.0_1 ===> locarna-2.0.0_1 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] Extracting autoconf-2.72: .......... done ===== Message from libsigsegv-2.14: -- Note that the stackoverflow handling functions of this library need procfs mounted on /proc. ===> locarna-2.0.0_1 depends on package: autoconf>=2.72 - found ===> Returning to build of locarna-2.0.0_1 ===> locarna-2.0.0_1 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 ===> locarna-2.0.0_1 depends on package: automake>=1.16.5 - found ===> Returning to build of locarna-2.0.0_1 ===> locarna-2.0.0_1 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 ===> locarna-2.0.0_1 depends on executable: libtoolize - found ===> Returning to build of locarna-2.0.0_1 ===> locarna-2.0.0_1 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> locarna-2.0.0_1 depends on shared library: libgmp.so - found (/usr/local/lib/libgmp.so) ===> locarna-2.0.0_1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> locarna-2.0.0_1 depends on shared library: libmpfr.so - found (/usr/local/lib/libmpfr.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for locarna-2.0.0_1 libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/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:47: installing 'config/compile' configure.ac:52: installing 'config/missing' src/Makefile.am: installing 'config/depcomp' 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 how to print strings... printf 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 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/local/bin/nm -B checking the name lister (/usr/local/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-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... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking for gawk... (cached) /usr/bin/awk checking command to parse /usr/local/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... 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... yes 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 whether gmake sets $(MAKE)... yes checking whether gmake supports the include directive... yes (GNU style) checking whether gmake supports nested variables... yes checking dependency style of cc... gcc3 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 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 dependency style of c++... gcc3 checking how to run the C++ preprocessor... c++ -E 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 how to run the C preprocessor... cpp checking whether c++ supports C++14 features by default... yes checking for perl... perl checking for pod2man... pod2man checking for doxygen... no configure: WARNING: doxygen not found - will not generate any doxygen documentation checking for perl... /usr/local/bin/perl checking for dot... no configure: WARNING: dot not found - will not generate graphics for doxygen documentation checking for pdflatex... no configure: WARNING: pdflatex not found - will not generate doxygen PDF documentation checking for makeindex... no configure: WARNING: makeindex not found - will not generate doxygen PDF documentation checking for egrep... /usr/bin/egrep checking for strdup... (cached) yes checking for pkg-config... true checking pkg-config is at least version 0.9.0... yes checking for RNAlib2 >= 2.5.1... yes configure: Get Vienna RNA configuration from pkg-config and remove -fno-lto. checking for vrna_C11_features in -lRNA... yes configure: VRNA_LIBS= -L/usr/local/lib -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp; VRNA_CFLAGS=-I/usr/local/include -I/usr/local/include/ViennaRNA -pthread checking whether to build with debug information... no checking for library containing expq... no configure: WARNING: Cannot find quadmath library: compile w/o quad-pf support. checking whether to link statically... no checking whether to link binaries dynamically to libLocARNA... no checking for _Bool... (cached) yes checking for stdbool.h that conforms to C99 or later... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating Makefile-benchmark config.status: creating src/Makefile config.status: creating src/Tests/Makefile config.status: creating src/Utils/Makefile config.status: creating Doc/Makefile config.status: creating Doc/man/Makefile config.status: creating lib/Makefile config.status: creating lib/perl/Makefile config.status: creating lib/perl/MLocarna/Makefile config.status: creating LocARNA-2.0.pc config.status: creating src/package_constants.hh config.status: creating Packaging/debian/control config.status: creating Packaging/rpm/locarna.spec config.status: creating src/config.h config.status: executing libtool commands config.status: executing depfiles commands =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for locarna-2.0.0_1 Making all in src gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' depbase=`echo ribosum2cc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT ribosum2cc.o -MD -MP -MF $depbase.Tpo -c -o ribosum2cc.o ribosum2cc.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo LocARNA/aligner.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT LocARNA/aligner.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/aligner.lo LocARNA/aligner.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT LocARNA/aligner.lo -MD -MP -MF LocARNA/.deps/aligner.Tpo -c LocARNA/aligner.cc -fPIC -DPIC -o LocARNA/.libs/aligner.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT LocARNA/aligner.lo -MD -MP -MF LocARNA/.deps/aligner.Tpo -c LocARNA/aligner.cc -o LocARNA/aligner.o >/dev/null 2>&1 depbase=`echo LocARNA/aligner_n.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT LocARNA/aligner_n.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/aligner_n.lo LocARNA/aligner_n.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT LocARNA/aligner_n.lo -MD -MP -MF LocARNA/.deps/aligner_n.Tpo -c LocARNA/aligner_n.cc -fPIC -DPIC -o LocARNA/.libs/aligner_n.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT LocARNA/aligner_n.lo -MD -MP -MF LocARNA/.deps/aligner_n.Tpo -c LocARNA/aligner_n.cc -o LocARNA/aligner_n.o >/dev/null 2>&1 depbase=`echo LocARNA/alignment.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT LocARNA/alignment.lo -MD -MP 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$depbase.Tpo -c -o LocARNA/rna_structure.lo LocARNA/rna_structure.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT LocARNA/rna_structure.lo -MD -MP -MF LocARNA/.deps/rna_structure.Tpo -c LocARNA/rna_structure.cc -fPIC -DPIC -o LocARNA/.libs/rna_structure.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT LocARNA/rna_structure.lo -MD -MP -MF LocARNA/.deps/rna_structure.Tpo -c LocARNA/rna_structure.cc -o LocARNA/rna_structure.o >/dev/null 2>&1 depbase=`echo LocARNA/scoring.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 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-DPIC -shared -nostdlib /usr/lib/crti.o /usr/lib/crtbeginS.o LocARNA/.libs/aligner.o LocARNA/.libs/aligner_n.o LocARNA/.libs/alignment.o LocARNA/.libs/anchor_constraints.o LocARNA/.libs/arc_matches.o LocARNA/.libs/aux.o LocARNA/.libs/basepairs.o LocARNA/.libs/confusion_matrix.o LocARNA/.libs/exact_matcher.o LocARNA/.libs/global_stopwatch.o LocARNA/.libs/infty_int.o LocARNA/.libs/edge_probs.o LocARNA/.libs/mcc_matrices.o LocARNA/.libs/multiple_alignment.o LocARNA/.libs/options.o LocARNA/.libs/ribofit.o LocARNA/.libs/ribosum.o LocARNA/.libs/rna_data.o LocARNA/.libs/rna_ensemble.o LocARNA/.libs/rna_structure.o LocARNA/.libs/scoring.o LocARNA/.libs/sequence.o LocARNA/.libs/sequence_annotation.o LocARNA/.libs/sparsification_mapper.o LocARNA/.libs/stopwatch.o LocARNA/.libs/stral_score.o LocARNA/.libs/trace_controller.o -L/usr/local/lib -lRNA -lgsl -lgslcblas -lpthread -lmpfr -lgmp -L/usr/lib -lc++ -lm -lc -lgcc -lgcc_s /usr/lib/crtendS.o /usr/lib/crtn.o -O2 -fstack-protector-strong -fstack-protector-strong -fopenmp -fopenmp -Wl,-soname -Wl,libLocARNA-2.0.so.1 -o .libs/libLocARNA-2.0.so.1.0.4 libtool: link: (cd ".libs" && rm -f "libLocARNA-2.0.so.1" && ln -s "libLocARNA-2.0.so.1.0.4" "libLocARNA-2.0.so.1") libtool: link: (cd ".libs" && rm -f "libLocARNA-2.0.so" && ln -s "libLocARNA-2.0.so.1.0.4" "libLocARNA-2.0.so") libtool: link: ar cr .libs/libLocARNA-2.0.a LocARNA/aligner.o LocARNA/aligner_n.o LocARNA/alignment.o LocARNA/anchor_constraints.o LocARNA/arc_matches.o LocARNA/aux.o LocARNA/basepairs.o LocARNA/confusion_matrix.o LocARNA/exact_matcher.o LocARNA/global_stopwatch.o LocARNA/infty_int.o LocARNA/edge_probs.o LocARNA/mcc_matrices.o LocARNA/multiple_alignment.o LocARNA/options.o LocARNA/ribofit.o LocARNA/ribosum.o LocARNA/rna_data.o LocARNA/rna_ensemble.o LocARNA/rna_structure.o LocARNA/scoring.o LocARNA/sequence.o LocARNA/sequence_annotation.o LocARNA/sparsification_mapper.o LocARNA/stopwatch.o LocARNA/stral_score.o LocARNA/trace_controller.o libtool: link: ranlib .libs/libLocARNA-2.0.a libtool: link: ( cd ".libs" && rm -f "libLocARNA-2.0.la" && ln -s "../libLocARNA-2.0.la" "libLocARNA-2.0.la" ) /bin/sh ../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -static -fstack-protector-strong -o ribosum2cc ribosum2cc.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -fstack-protector-strong -o ribosum2cc ribosum2cc.o -fopenmp ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lgsl -lgslcblas -lpthread -lmpfr -lgmp -fopenmp ./ribosum2cc Ribosum85_60 "../Data/Matrices/RIBOSUM85_60" LocARNA/ribosum85_60.icc gmake all-recursive gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' Making all in Utils gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Utils' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Utils' Making all in . gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' depbase=`echo locarna.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT locarna.o -MD -MP -MF $depbase.Tpo -c -o locarna.o locarna.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/sh ../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -static -fstack-protector-strong -o locarna.bin locarna.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -fstack-protector-strong -o locarna.bin locarna.o -fopenmp ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lgsl -lgslcblas -lpthread -lmpfr -lgmp -fopenmp depbase=`echo locarna_p.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT locarna_p.o -MD -MP -MF $depbase.Tpo -c -o locarna_p.o locarna_p.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/sh ../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -static -fstack-protector-strong -o locarna_p locarna_p.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -fstack-protector-strong -o locarna_p locarna_p.o -fopenmp ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lgsl -lgslcblas -lpthread -lmpfr -lgmp -fopenmp depbase=`echo fit.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT fit.o -MD -MP -MF $depbase.Tpo -c -o fit.o fit.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo LocARNA/fitonoff.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT LocARNA/fitonoff.o -MD -MP -MF $depbase.Tpo -c -o LocARNA/fitonoff.o LocARNA/fitonoff.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/sh ../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -static -fstack-protector-strong -o locarnap_fit fit.o LocARNA/fitonoff.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -fstack-protector-strong -o locarnap_fit fit.o LocARNA/fitonoff.o -fopenmp ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lgsl -lgslcblas -lpthread -lmpfr -lgmp -fopenmp depbase=`echo deviation.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT deviation.o -MD -MP -MF $depbase.Tpo -c -o deviation.o deviation.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/sh ../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -static -fstack-protector-strong -o locarna_deviation deviation.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -fstack-protector-strong -o locarna_deviation deviation.o -fopenmp ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lgsl -lgslcblas -lpthread -lmpfr -lgmp -fopenmp depbase=`echo locarna_rnafold_pp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT locarna_rnafold_pp.o -MD -MP -MF $depbase.Tpo -c -o locarna_rnafold_pp.o locarna_rnafold_pp.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/sh ../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -static -fstack-protector-strong -o locarna_rnafold_pp locarna_rnafold_pp.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -fstack-protector-strong -o locarna_rnafold_pp locarna_rnafold_pp.o -fopenmp ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lgsl -lgslcblas -lpthread -lmpfr -lgmp -fopenmp depbase=`echo exparna_p.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT exparna_p.o -MD -MP -MF $depbase.Tpo -c -o exparna_p.o exparna_p.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/sh ../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -static -fstack-protector-strong -o exparna_p exparna_p.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -fstack-protector-strong -o exparna_p exparna_p.o -fopenmp ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lgsl -lgslcblas -lpthread -lmpfr -lgmp -fopenmp depbase=`echo sparse.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -MT sparse.o -MD -MP -MF $depbase.Tpo -c -o sparse.o sparse.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/sh ../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -static -fstack-protector-strong -o sparse sparse.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -fstack-protector-strong -o sparse sparse.o -fopenmp ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lgsl -lgslcblas -lpthread -lmpfr -lgmp -fopenmp gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' Making all in Tests gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Tests' cp ../../Data/Examples/archaea.aln archaea.aln cp ../../Data/Examples/archaea-aln.fa archaea-aln.fa cp ../../Data/Examples/archaea-wrong.fa archaea-wrong.fa gmake all-am gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Tests' gmake[4]: Nothing to be done for 'all-am'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Tests' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Tests' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' Making all in lib gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib' Making all in perl gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl' Making all in MLocarna gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl/MLocarna' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl/MLocarna' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl' gmake[3]: Nothing to be done for 'all-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib' gmake[2]: Nothing to be done for 'all-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib' Making all in Doc gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc' Making all in man gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc/man' gmake[2]: Nothing to be done for 'all'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc/man' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc' gmake[2]: Nothing to be done for 'all-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc' gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0' gmake[1]: Nothing to be done for 'all-am'. gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0' =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> locarna-2.0.0_1 depends on package: perl5>=5.36<5.37 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for locarna-2.0.0_1 ===> Generating temporary packing list if test -z 'strip'; then \ gmake INSTALL_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/config/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/config/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ install; \ else \ gmake INSTALL_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/config/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/config/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ "INSTALL_PROGRAM_ENV=STRIPPROG='strip'" install; \ fi gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0' Making install in src gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' gmake install-recursive gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' Making install in Utils gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Utils' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Utils' /bin/mkdir -p '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/bin' install -m 555 mlocarna locarnate locarna-motif-scan plot-bmprobs gen-reliab-dot.pl reliability-profile.pl aln2fa.pl alnsel.pl locarnap-realign-all.pl locarnap-revisit-RNAz-hits.pl locarnap-predict-and-plot.pl locarnap-revcomp.pl RNAz.pm LocARNA_RNAz.pm dot2pp pp2dot mlocarna_nnames locarna-mea.pl average-dot.pl aln-seqs.pl exploc_p locarna_mcc benchmark-plot.R '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/bin' gmake[5]: Nothing to be done for 'install-data-am'. gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Utils' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Utils' Making install in . gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' /bin/mkdir -p '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c -s libLocARNA-2.0.la '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libLocARNA-2.0.so.1.0.4 /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib/libLocARNA-2.0.so.1.0.4 libtool: install: strip --strip-unneeded /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib/libLocARNA-2.0.so.1.0.4 libtool: install: (cd /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib && { ln -s -f libLocARNA-2.0.so.1.0.4 libLocARNA-2.0.so.1 || { rm -f libLocARNA-2.0.so.1 && ln -s libLocARNA-2.0.so.1.0.4 libLocARNA-2.0.so.1; }; }) libtool: install: (cd /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib && { ln -s -f libLocARNA-2.0.so.1.0.4 libLocARNA-2.0.so || { rm -f libLocARNA-2.0.so && ln -s libLocARNA-2.0.so.1.0.4 libLocARNA-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libLocARNA-2.0.lai /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib/libLocARNA-2.0.la libtool: install: /usr/bin/install -c .libs/libLocARNA-2.0.a /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib/libLocARNA-2.0.a libtool: install: strip --strip-debug /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib/libLocARNA-2.0.a libtool: install: chmod 644 /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib/libLocARNA-2.0.a libtool: install: ranlib /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib/libLocARNA-2.0.a libtool: warning: remember to run 'libtool --finish /usr/local/lib' /bin/mkdir -p '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/bin' STRIPPROG='strip' /bin/sh ../libtool --mode=install /bin/sh /wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/config/install-sh -c -s locarna.bin '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/bin/./locarna' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/config/install-sh -c -s locarna.bin /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/bin/./locarna STRIPPROG='strip' /bin/sh ../libtool --mode=install /bin/sh /wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/config/install-sh -c -s locarna_p locarnap_fit locarna_deviation locarna_rnafold_pp exparna_p sparse ribosum2cc '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/bin' libtool: install: /bin/sh /wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/config/install-sh -c -s locarna_p /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/bin/locarna_p libtool: install: /bin/sh /wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/config/install-sh -c -s locarnap_fit /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/bin/locarnap_fit libtool: install: /bin/sh /wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/config/install-sh -c -s locarna_deviation /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/bin/locarna_deviation libtool: install: /bin/sh /wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/config/install-sh -c -s locarna_rnafold_pp /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/bin/locarna_rnafold_pp libtool: install: /bin/sh /wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/config/install-sh -c -s exparna_p /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/bin/exparna_p libtool: install: /bin/sh /wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/config/install-sh -c -s sparse /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/bin/sparse libtool: install: /bin/sh /wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/config/install-sh -c -s ribosum2cc /wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/bin/ribosum2cc /bin/mkdir -p '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/include/LocARNA-2.0' /bin/mkdir -p '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/include/LocARNA-2.0/LocARNA' install -m 0644 LocARNA/aligner.hh LocARNA/aligner_impl.hh LocARNA/aligner_n.hh LocARNA/aligner_p.hh LocARNA/aligner_p.icc LocARNA/aligner_params.hh LocARNA/aligner_restriction.hh LocARNA/alignment.hh LocARNA/alignment_impl.hh LocARNA/alphabet.hh LocARNA/alphabet.icc LocARNA/anchor_constraints.hh LocARNA/arc_matches.hh LocARNA/aux.hh LocARNA/base_pair_filter.hh LocARNA/basepairs.hh LocARNA/confusion_matrix.hh LocARNA/discrete_distribution.hh LocARNA/exact_matcher.hh LocARNA/ext_rna_data.hh LocARNA/ext_rna_data_impl.hh LocARNA/free_endgaps.hh LocARNA/global_stopwatch.hh LocARNA/infty_int.hh LocARNA/main_helper.icc LocARNA/edge_probs.hh LocARNA/edge_probs.icc LocARNA/matrices.hh LocARNA/matrix.hh LocARNA/mcc_matrices.hh LocARNA/multiple_alignment.hh LocARNA/named_arguments.hh LocARNA/options.hh LocARNA/pfold_params.hh LocARNA/quadmath.hh LocARNA/ribofit.hh LocARNA/ribofit_will2014.icc LocARNA/ribofit_will2014.ihh LocARNA/ribosum.hh LocARNA/ribosum85_60.icc '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/include/LocARNA-2.0/LocARNA' /bin/mkdir -p '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/include/LocARNA-2.0/LocARNA' install -m 0644 LocARNA/rna_data.hh LocARNA/rna_data_impl.hh LocARNA/rna_ensemble.hh LocARNA/rna_ensemble_impl.hh LocARNA/rna_structure.hh LocARNA/scoring.hh LocARNA/scoring_fwd.hh LocARNA/sequence.hh LocARNA/sequence_annotation.hh LocARNA/sparse_matrix.hh LocARNA/sparse_vector.hh LocARNA/sparse_vector_base.hh LocARNA/sparsification_mapper.hh LocARNA/std_help_text.ihh LocARNA/stopwatch.hh LocARNA/stral_score.hh LocARNA/string1.hh LocARNA/trace_controller.hh LocARNA/tuples.hh LocARNA/zip.hh '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/include/LocARNA-2.0/LocARNA' /bin/mkdir -p '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib/pkgconfig' install -m 0644 ../LocARNA-2.0.pc '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib/pkgconfig' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' Making install in Tests gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Tests' gmake install-am gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Tests' gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Tests' gmake[6]: Nothing to be done for 'install-exec-am'. gmake[6]: Nothing to be done for 'install-data-am'. gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Tests' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Tests' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src/Tests' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' Making install in lib gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib' Making install in perl gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl' Making install in MLocarna gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl/MLocarna' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl/MLocarna' gmake[5]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib/perl/MLocarna' install -m 555 SparseMatrix.pm Tree.pm MatchProbs.pm Aux.pm threaded.pm unthreaded.pm PairwiseAligners.pm NameNormalizer.pm '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib/perl/MLocarna' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl/MLocarna' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl/MLocarna' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl' gmake[5]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib/perl' install -m 555 MLocarna.pm '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/lib/perl' gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib/perl' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/lib' Making install in Doc gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc' Making install in man gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc/man' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc/man' gmake[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/share/man/man1' install -m 0644 exparna_p.1 locarna_deviation.1 locarna_p.1 locarnap_fit.1 locarna_rnafold_pp.1 ribosum2cc.1 sparse.1 locarna.1 aln2fa.pl.1 alnsel.pl.1 aln-seqs.pl.1 average-dot.pl.1 dot2pp.1 exploc_p.1 gen-reliab-dot.pl.1 locarna_mcc.1 locarna-mea.pl.1 locarna-motif-scan.1 locarnap-predict-and-plot.pl.1 locarnap-realign-all.pl.1 locarnap-revcomp.pl.1 locarnap-revisit-RNAz-hits.pl.1 locarnate.1 mlocarna.1 mlocarna_nnames.1 plot-bmprobs.1 pp2dot.1 reliability-profile.pl.1 '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/share/man/man1' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc/man' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc/man' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/Doc' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0' gmake[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/share/locarna/Matrices' install -m 0644 Data/Matrices/RIBOSUM85_60 '/wrkdirs/usr/ports/biology/locarna/work/stage/usr/local/share/locarna/Matrices' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0' ====> 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=2024-04-05T03:05:23+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=c779176e8a' '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 locarna-2.0.0_1 ===> Building locarna-2.0.0_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for locarna-2.0.0_1 build of biology/locarna | locarna-2.0.0_1 ended at Fri Apr 5 04:11:08 BST 2024 build time: 00:05:46