=>> Building biology/locarna build started at Thu Mar 12 20:11:14 EDT 2026 port directory: /usr/ports/biology/locarna package name: locarna-2.0.0_2 building for: FreeBSD pkg.DaveG.ca 14.4-RELEASE FreeBSD 14.4-RELEASE 1404000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1188 Feb 17 19:06 /usr/ports/biology/locarna/Makefile Ports top last git commit: 26b198eb3ee3 Ports top unclean checkout: no Port dir last git commit: 2e4f3d1acf81 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1404000 Job Id: 04 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1404000 UNAME_v=FreeBSD 14.4-RELEASE 1404000 UNAME_r=14.4-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_4_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 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=/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 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=/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=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 " CXXSTD=c++14 BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=14.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.0 PERL_VER=5.42 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.42 DOCSDIR="share/doc/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--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> locarna-2.0.0_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> locarna-2.0.0_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of locarna-2.0.0_2 =========================================================================== =================================================== ===== 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_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by locarna-2.0.0_2 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_2 for building ===> Extracting for locarna-2.0.0_2 => 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_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> locarna-2.0.0_2 depends on file: /usr/local/lib/libRNA.a - not found ===> Installing existing package /packages/All/viennarna-2.7.0_3.pkg [pkg.DaveG.ca] Installing viennarna-2.7.0_3... [pkg.DaveG.ca] `-- Installing dlib-cpp-20.0_1... [pkg.DaveG.ca] | `-- Installing giflib-5.2.2... [pkg.DaveG.ca] | `-- Extracting giflib-5.2.2: .......... done [pkg.DaveG.ca] | `-- Installing jpeg-turbo-3.1.3... [pkg.DaveG.ca] | `-- Extracting jpeg-turbo-3.1.3: .......... done [pkg.DaveG.ca] | `-- Installing libICE-1.1.2,1... [pkg.DaveG.ca] | `-- Extracting libICE-1.1.2,1: .......... done [pkg.DaveG.ca] | `-- Installing libSM-1.2.6,1... [pkg.DaveG.ca] | `-- Extracting libSM-1.2.6,1: ........ done [pkg.DaveG.ca] | `-- Installing libX11-1.8.12,1... [pkg.DaveG.ca] | | `-- Installing libxcb-1.17.0... [pkg.DaveG.ca] | | `-- Installing libXau-1.0.12... [pkg.DaveG.ca] | | `-- Extracting libXau-1.0.12: .......... done [pkg.DaveG.ca] | | `-- Installing libXdmcp-1.1.5... [pkg.DaveG.ca] | | | `-- Installing xorgproto-2024.1... [pkg.DaveG.ca] | | | `-- Extracting xorgproto-2024.1: .......... done [pkg.DaveG.ca] | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg.DaveG.ca] | | `-- Extracting libxcb-1.17.0: .......... done [pkg.DaveG.ca] | `-- Extracting libX11-1.8.12,1: .......... done [pkg.DaveG.ca] | `-- Installing libXext-1.3.6,1... [pkg.DaveG.ca] | `-- Extracting libXext-1.3.6,1: .......... done [pkg.DaveG.ca] | `-- Installing png-1.6.55... [pkg.DaveG.ca] | `-- Extracting png-1.6.55: .......... done [pkg.DaveG.ca] | `-- Installing sqlite3-3.50.4_2,1... [pkg.DaveG.ca] | | `-- Installing libedit-3.1.20251016_1,1... [pkg.DaveG.ca] | | `-- Extracting libedit-3.1.20251016_1,1: .......... done [pkg.DaveG.ca] | `-- Extracting sqlite3-3.50.4_2,1: .......... done [pkg.DaveG.ca] `-- Extracting dlib-cpp-20.0_1: .......... done [pkg.DaveG.ca] `-- Installing gcc14-14.2.0_4... [pkg.DaveG.ca] | `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | | `-- Installing mpfr-4.2.2,1... [pkg.DaveG.ca] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg.DaveG.ca] | `-- Extracting mpc-1.3.1_1: ...... done [pkg.DaveG.ca] `-- Extracting gcc14-14.2.0_4: .......... done [pkg.DaveG.ca] `-- Installing gsl-2.8... [pkg.DaveG.ca] `-- Extracting gsl-2.8: .......... done [pkg.DaveG.ca] `-- Installing lapack-3.12.1... [pkg.DaveG.ca] | `-- Installing blas-3.12.1... [pkg.DaveG.ca] | `-- Extracting blas-3.12.1: ..... done [pkg.DaveG.ca] `-- Extracting lapack-3.12.1: .......... done [pkg.DaveG.ca] `-- Installing perl5-5.42.0_1... [pkg.DaveG.ca] `-- Extracting perl5-5.42.0_1: .......... done [pkg.DaveG.ca] Extracting viennarna-2.7.0_3: .......... done ===== Message from gcc14-14.2.0_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/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> locarna-2.0.0_2 depends on file: /usr/local/lib/libRNA.a - found ===> Returning to build of locarna-2.0.0_2 ===> locarna-2.0.0_2 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> locarna-2.0.0_2 depends on package: gmake>=4.4.1 - found ===> Returning to build of locarna-2.0.0_2 ===> locarna-2.0.0_2 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.4.3,1.pkg [pkg.DaveG.ca] Installing pkgconf-2.4.3,1... [pkg.DaveG.ca] Extracting pkgconf-2.4.3,1: .......... done ===> locarna-2.0.0_2 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of locarna-2.0.0_2 ===> locarna-2.0.0_2 depends on package: autoconf>=2.72_1 - not found ===> Installing existing package /packages/All/autoconf-2.72_1.pkg [pkg.DaveG.ca] Installing autoconf-2.72_1... [pkg.DaveG.ca] `-- Installing autoconf-switch-20220527... [pkg.DaveG.ca] `-- Extracting autoconf-switch-20220527: ....... done [pkg.DaveG.ca] `-- Installing m4-1.4.20,1... [pkg.DaveG.ca] `-- Extracting m4-1.4.20,1: .......... done [pkg.DaveG.ca] Extracting autoconf-2.72_1: .......... done ===> locarna-2.0.0_2 depends on package: autoconf>=2.72_1 - found ===> Returning to build of locarna-2.0.0_2 ===> locarna-2.0.0_2 depends on package: automake>=1.18.1 - not found ===> Installing existing package /packages/All/automake-1.18.1.pkg [pkg.DaveG.ca] Installing automake-1.18.1... [pkg.DaveG.ca] Extracting automake-1.18.1: .......... done ===> locarna-2.0.0_2 depends on package: automake>=1.18.1 - found ===> Returning to build of locarna-2.0.0_2 ===> locarna-2.0.0_2 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.5.4_1.pkg [pkg.DaveG.ca] Installing libtool-2.5.4_1... [pkg.DaveG.ca] Extracting libtool-2.5.4_1: .......... done ===> locarna-2.0.0_2 depends on executable: libtoolize - found ===> Returning to build of locarna-2.0.0_2 ===> locarna-2.0.0_2 depends on package: perl5>=5.42.r<5.43 - found ===> locarna-2.0.0_2 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc14 create symlink for gcc14 (world) create symlink for g++14 create symlink for g++14 (world) create symlink for cpp14 create symlink for cpp14 (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> locarna-2.0.0_2 depends on file: /usr/local/bin/ccache - found ===> Returning to build of locarna-2.0.0_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> locarna-2.0.0_2 depends on shared library: libgmp.so - found (/usr/local/lib/libgmp.so) ===> locarna-2.0.0_2 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> locarna-2.0.0_2 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_2 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-freebsd14.4 checking host system type... amd64-portbld-freebsd14.4 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-freebsd14.4 file names to amd64-portbld-freebsd14.4 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd14.4 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... ranlib checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking 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... freebsd14.4 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking whether /usr/local/bin/gmake supports nested variables... yes checking xargs -n works... yes checking whether UID '0' is supported by ustar format... yes checking whether GID '0' is supported by ustar format... yes checking how to create a ustar tar archive... (cached) /usr/bin/tar checking 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... freebsd14.4 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 -lomp -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_2 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 $depbase.Plo depbase=`echo LocARNA/aligner_n.lo | sed 's|[^/]*$|.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 $depbase.Plo depbase=`echo LocARNA/alignment.lo | sed 's|[^/]*$|.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 -MF $depbase.Tpo -c -o LocARNA/alignment.lo LocARNA/alignment.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo LocARNA/anchor_constraints.lo | sed 's|[^/]*$|.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/anchor_constraints.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/anchor_constraints.lo LocARNA/anchor_constraints.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo LocARNA/arc_matches.lo | sed 's|[^/]*$|.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/arc_matches.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/arc_matches.lo LocARNA/arc_matches.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo LocARNA/aux.lo | sed 's|[^/]*$|.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/aux.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/aux.lo LocARNA/aux.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo LocARNA/basepairs.lo | sed 's|[^/]*$|.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/basepairs.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/basepairs.lo LocARNA/basepairs.cc &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo LocARNA/confusion_matrix.lo | sed 's|[^/]*$|.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/confusion_matrix.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/confusion_matrix.lo LocARNA/confusion_matrix.cc &&\ mv -f $depbase.Tpo 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LocARNA/.deps/mcc_matrices.Tpo -c LocARNA/mcc_matrices.cc -fPIC -DPIC -o LocARNA/.libs/mcc_matrices.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/global_stopwatch.lo -MD -MP -MF LocARNA/.deps/global_stopwatch.Tpo -c LocARNA/global_stopwatch.cc -fPIC -DPIC -o LocARNA/.libs/global_stopwatch.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/basepairs.lo -MD -MP -MF LocARNA/.deps/basepairs.Tpo -c LocARNA/basepairs.cc -fPIC -DPIC -o LocARNA/.libs/basepairs.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/arc_matches.lo -MD -MP -MF LocARNA/.deps/arc_matches.Tpo -c LocARNA/arc_matches.cc -fPIC -DPIC -o LocARNA/.libs/arc_matches.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/alignment.lo -MD -MP -MF LocARNA/.deps/alignment.Tpo -c LocARNA/alignment.cc -fPIC -DPIC -o LocARNA/.libs/alignment.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/edge_probs.lo -MD -MP -MF LocARNA/.deps/edge_probs.Tpo -c LocARNA/edge_probs.cc -fPIC -DPIC -o LocARNA/.libs/edge_probs.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/sparsification_mapper.lo -MD -MP -MF LocARNA/.deps/sparsification_mapper.Tpo -c LocARNA/sparsification_mapper.cc -fPIC -DPIC -o LocARNA/.libs/sparsification_mapper.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/sequence.lo -MD -MP -MF LocARNA/.deps/sequence.Tpo -c LocARNA/sequence.cc -fPIC -DPIC -o LocARNA/.libs/sequence.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/ribofit.lo -MD -MP -MF LocARNA/.deps/ribofit.Tpo -c LocARNA/ribofit.cc -fPIC -DPIC -o LocARNA/.libs/ribofit.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/confusion_matrix.lo -MD -MP -MF LocARNA/.deps/confusion_matrix.Tpo -c LocARNA/confusion_matrix.cc -fPIC -DPIC -o LocARNA/.libs/confusion_matrix.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/stral_score.lo -MD -MP -MF LocARNA/.deps/stral_score.Tpo -c LocARNA/stral_score.cc -fPIC -DPIC -o LocARNA/.libs/stral_score.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/infty_int.lo -MD -MP -MF LocARNA/.deps/infty_int.Tpo -c LocARNA/infty_int.cc -fPIC -DPIC -o LocARNA/.libs/infty_int.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/multiple_alignment.lo -MD -MP -MF LocARNA/.deps/multiple_alignment.Tpo -c LocARNA/multiple_alignment.cc -fPIC -DPIC -o LocARNA/.libs/multiple_alignment.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/ribosum.lo -MD -MP -MF LocARNA/.deps/ribosum.Tpo -c LocARNA/ribosum.cc -fPIC -DPIC -o LocARNA/.libs/ribosum.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/anchor_constraints.lo -MD -MP -MF LocARNA/.deps/anchor_constraints.Tpo -c LocARNA/anchor_constraints.cc -fPIC -DPIC -o LocARNA/.libs/anchor_constraints.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/scoring.lo -MD -MP -MF LocARNA/.deps/scoring.Tpo -c LocARNA/scoring.cc -fPIC -DPIC -o LocARNA/.libs/scoring.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/options.lo -MD -MP -MF LocARNA/.deps/options.Tpo -c LocARNA/options.cc -fPIC -DPIC -o LocARNA/.libs/options.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 -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_ensemble.lo -MD -MP -MF LocARNA/.deps/rna_ensemble.Tpo -c LocARNA/rna_ensemble.cc -fPIC -DPIC -o LocARNA/.libs/rna_ensemble.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/stopwatch.lo -MD -MP -MF LocARNA/.deps/stopwatch.Tpo -c LocARNA/stopwatch.cc -fPIC -DPIC -o LocARNA/.libs/stopwatch.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/sequence_annotation.lo -MD -MP -MF LocARNA/.deps/sequence_annotation.Tpo -c LocARNA/sequence_annotation.cc -fPIC -DPIC -o LocARNA/.libs/sequence_annotation.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/trace_controller.lo -MD -MP -MF LocARNA/.deps/trace_controller.Tpo -c LocARNA/trace_controller.cc -fPIC -DPIC -o LocARNA/.libs/trace_controller.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_data.lo -MD -MP -MF LocARNA/.deps/rna_data.Tpo -c LocARNA/rna_data.cc -fPIC -DPIC -o LocARNA/.libs/rna_data.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/global_stopwatch.lo -MD -MP -MF LocARNA/.deps/global_stopwatch.Tpo -c LocARNA/global_stopwatch.cc -o LocARNA/global_stopwatch.o >/dev/null 2>&1 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/infty_int.lo -MD -MP -MF LocARNA/.deps/infty_int.Tpo -c LocARNA/infty_int.cc -o LocARNA/infty_int.o >/dev/null 2>&1 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/confusion_matrix.lo -MD -MP -MF LocARNA/.deps/confusion_matrix.Tpo -c LocARNA/confusion_matrix.cc -o LocARNA/confusion_matrix.o >/dev/null 2>&1 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/ribofit.lo -MD -MP -MF LocARNA/.deps/ribofit.Tpo -c LocARNA/ribofit.cc -o LocARNA/ribofit.o >/dev/null 2>&1 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/stopwatch.lo -MD -MP -MF LocARNA/.deps/stopwatch.Tpo -c LocARNA/stopwatch.cc -o LocARNA/stopwatch.o >/dev/null 2>&1 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/sequence.lo -MD -MP -MF LocARNA/.deps/sequence.Tpo -c LocARNA/sequence.cc -o LocARNA/sequence.o >/dev/null 2>&1 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/sequence_annotation.lo -MD -MP -MF LocARNA/.deps/sequence_annotation.Tpo -c LocARNA/sequence_annotation.cc -o LocARNA/sequence_annotation.o >/dev/null 2>&1 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/mcc_matrices.lo -MD -MP -MF LocARNA/.deps/mcc_matrices.Tpo -c LocARNA/mcc_matrices.cc -o LocARNA/mcc_matrices.o >/dev/null 2>&1 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/aux.lo -MD -MP -MF LocARNA/.deps/aux.Tpo -c LocARNA/aux.cc -o LocARNA/aux.o >/dev/null 2>&1 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/stral_score.lo -MD -MP -MF LocARNA/.deps/stral_score.Tpo -c LocARNA/stral_score.cc -o LocARNA/stral_score.o >/dev/null 2>&1 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/sparsification_mapper.lo -MD -MP -MF LocARNA/.deps/sparsification_mapper.Tpo -c LocARNA/sparsification_mapper.cc -o LocARNA/sparsification_mapper.o >/dev/null 2>&1 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/anchor_constraints.lo -MD -MP -MF LocARNA/.deps/anchor_constraints.Tpo -c LocARNA/anchor_constraints.cc -o LocARNA/anchor_constraints.o >/dev/null 2>&1 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/options.lo -MD -MP -MF LocARNA/.deps/options.Tpo -c LocARNA/options.cc -o LocARNA/options.o >/dev/null 2>&1 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 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/alignment.lo -MD -MP -MF LocARNA/.deps/alignment.Tpo -c LocARNA/alignment.cc -o LocARNA/alignment.o >/dev/null 2>&1 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/edge_probs.lo -MD -MP -MF LocARNA/.deps/edge_probs.Tpo -c LocARNA/edge_probs.cc -o LocARNA/edge_probs.o >/dev/null 2>&1 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/ribosum.lo -MD -MP -MF LocARNA/.deps/ribosum.Tpo -c LocARNA/ribosum.cc -o LocARNA/ribosum.o >/dev/null 2>&1 LocARNA/scoring.cc:57:29: warning: 'bind2nd, long>' is deprecated [-Wdeprecated-declarations] 57 | std::bind2nd(std::minus(), x)); | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, long>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ LocARNA/scoring.cc:61:26: warning: 'bind2nd, long>' is deprecated [-Wdeprecated-declarations] 61 | m.transform(std::bind2nd(std::minus(), x)); | ^ /usr/include/c++/v1/__functional/binder2nd.h:45:1: note: 'bind2nd, long>' has been explicitly marked deprecated here 45 | _LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_HIDE_FROM_ABI binder2nd<_Operation> | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 2 warnings generated. 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/scoring.lo -MD -MP -MF LocARNA/.deps/scoring.Tpo -c LocARNA/scoring.cc -o LocARNA/scoring.o >/dev/null 2>&1 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/trace_controller.lo -MD -MP -MF LocARNA/.deps/trace_controller.Tpo -c LocARNA/trace_controller.cc -o LocARNA/trace_controller.o >/dev/null 2>&1 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_ensemble.lo -MD -MP -MF LocARNA/.deps/rna_ensemble.Tpo -c LocARNA/rna_ensemble.cc -o LocARNA/rna_ensemble.o >/dev/null 2>&1 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/arc_matches.lo -MD -MP -MF LocARNA/.deps/arc_matches.Tpo -c LocARNA/arc_matches.cc -o LocARNA/arc_matches.o >/dev/null 2>&1 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/basepairs.lo -MD -MP -MF LocARNA/.deps/basepairs.Tpo -c LocARNA/basepairs.cc -o LocARNA/basepairs.o >/dev/null 2>&1 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 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 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/multiple_alignment.lo -MD -MP -MF LocARNA/.deps/multiple_alignment.Tpo -c LocARNA/multiple_alignment.cc -o LocARNA/multiple_alignment.o >/dev/null 2>&1 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_data.lo -MD -MP -MF LocARNA/.deps/rna_data.Tpo -c LocARNA/rna_data.cc -o LocARNA/rna_data.o >/dev/null 2>&1 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/exact_matcher.lo -MD -MP -MF LocARNA/.deps/exact_matcher.Tpo -c LocARNA/exact_matcher.cc -o LocARNA/exact_matcher.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -version-info 1:4:0 -o libLocARNA-2.0.la -rpath /usr/local/lib LocARNA/aligner.lo LocARNA/aligner_n.lo LocARNA/alignment.lo LocARNA/anchor_constraints.lo LocARNA/arc_matches.lo LocARNA/aux.lo LocARNA/basepairs.lo LocARNA/confusion_matrix.lo LocARNA/exact_matcher.lo LocARNA/global_stopwatch.lo LocARNA/infty_int.lo LocARNA/edge_probs.lo LocARNA/mcc_matrices.lo LocARNA/multiple_alignment.lo LocARNA/options.lo LocARNA/ribofit.lo LocARNA/ribosum.lo LocARNA/rna_data.lo LocARNA/rna_ensemble.lo LocARNA/rna_structure.lo LocARNA/scoring.lo LocARNA/sequence.lo LocARNA/sequence_annotation.lo LocARNA/sparsification_mapper.lo LocARNA/stopwatch.lo LocARNA/stral_score.lo LocARNA/trace_controller.lo -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -fPIC -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 -lomp -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 -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 -o ribosum2cc ribosum2cc.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -o ribosum2cc ribosum2cc.o ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp ./ribosum2cc Ribosum85_60 "../Data/Matrices/RIBOSUM85_60" LocARNA/ribosum85_60.icc /usr/local/bin/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 $depbase.Po depbase=`echo locarna_p.o | sed 's|[^/]*$|.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 $depbase.Po depbase=`echo fit.o | sed 's|[^/]*$|.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 $depbase.Po depbase=`echo deviation.o | sed 's|[^/]*$|.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 $depbase.Po depbase=`echo locarna_rnafold_pp.o | sed 's|[^/]*$|.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 $depbase.Po depbase=`echo exparna_p.o | sed 's|[^/]*$|.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 $depbase.Po depbase=`echo sparse.o | sed 's|[^/]*$|.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 -o locarnap_fit fit.o LocARNA/fitonoff.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp /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 -o locarna_deviation deviation.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp /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 -o locarna_rnafold_pp locarna_rnafold_pp.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp /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 -o exparna_p exparna_p.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -o locarna_deviation deviation.o ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -o locarnap_fit fit.o LocARNA/fitonoff.o ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -o locarna_rnafold_pp locarna_rnafold_pp.o ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -o exparna_p exparna_p.o ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp /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 -o locarna.bin locarna.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp /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 -o locarna_p locarna_p.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp /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 -o sparse sparse.o libLocARNA-2.0.la -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -o sparse sparse.o ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -o locarna.bin locarna.o ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -std=c++14 -o locarna_p locarna_p.o ./.libs/libLocARNA-2.0.a -L/usr/local/lib -lRNA -lomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp 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 /usr/local/bin/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_2 depends on package: perl5>=5.42.r<5.43 - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for locarna-2.0.0_2 ===> Generating temporary packing list if test -z 'strip'; then \ /usr/local/bin/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 \ /usr/local/bin/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' /usr/local/bin/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' /usr/local/bin/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=2026-03-13T00:11:14+0000' 'PKG_NOTE_ports_top_git_hash=26b198eb3ee3' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=2e4f3d1acf81' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for locarna-2.0.0_2 ===> Building locarna-2.0.0_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for locarna-2.0.0_2 build of biology/locarna | locarna-2.0.0_2 ended at Thu Mar 12 20:13:07 EDT 2026 build time: 00:01:54