[exp - 140amd64-default-build-as-user][biology/locarna] Failed for locarna-2.0.0 in build
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Date: Wed, 13 Dec 2023 16:43:41 UTC
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Log URL: https://pkg-status.freebsd.org/package19/data/140amd64-default-build-as-user/bb504ccec5fc/logs/locarna-2.0.0.log Build URL: https://pkg-status.freebsd.org/package19/build.html?mastername=140amd64-default-build-as-user&build=bb504ccec5fc Log: =>> Building biology/locarna build started at Wed Dec 13 16:41:31 UTC 2023 port directory: /usr/ports/biology/locarna package name: locarna-2.0.0 building for: FreeBSD 140amd64-default-build-as-user-job-04 14.0-RELEASE-p2 FreeBSD 14.0-RELEASE-p2 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1014 Jul 18 00:06 /usr/ports/biology/locarna/Makefile Ports top last git commit: bb504ccec5f Ports top unclean checkout: no Port dir last git commit: 2ce2ca5b614 Port dir unclean checkout: no Poudriere version: poudriere-git-3.3.0-1258-gbc38e2e6 Host OSVERSION: 1500006 Jail OSVERSION: 1400097 Job Id: 04 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400097 UNAME_v=FreeBSD 14.0-RELEASE-p2 UNAME_r=14.0-RELEASE-p2 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 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.3.0-1258-gbc38e2e6 MASTERMNT=/poudriere/data/.m/140amd64-default-build-as-user/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/poudriere/data/.m/140amd64-default-build-as-user/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=140amd64-default-build-as-user SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/poudriere/data/.m/140amd64-default-build-as-user/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.3.0-1258-gbc38e2e6 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=/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=2.71 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=2.71 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 " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="i nstall -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=14.0 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 #### #### # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" ---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-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> locarna-2.0.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9.pkg [140amd64-default-build-as-user-job-04] Installing pkg-1.20.9... [140amd64-default-build-as-user-job-04] Extracting pkg-1.20.9: .......... done ===> locarna-2.0.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of locarna-2.0.0 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by locarna-2.0.0 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by locarna-2.0.0 for building => SHA256 Checksum OK for locarna-2.0.0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by locarna-2.0.0 for building ===> Extracting for locarna-2.0.0 => SHA256 Checksum OK for locarna-2.0.0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for locarna-2.0.0 =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> locarna-2.0.0 depends on file: /usr/local/lib/libRNA.a - not found ===> Installing existing package /packages/All/viennarna-2.6.4.pkg [140amd64-default-build-as-user-job-04] Installing viennarna-2.6.4... [140amd64-default-build-as-user-job-04] `-- Installing gcc12-12.2.0_7... [140amd64-default-build-as-user-job-04] | `-- Installing binutils-2.40_4,1... [140amd64-default-build-as-user-job-04] | | `-- Installing gettext-runtime-0.22.3... [140amd64-default-build-as-user-job-04] | | `-- Installing indexinfo-0.3.1... [140amd64-default-build-as-user-job-04] | | `-- Extracting indexinfo-0.3.1: .... done [140amd64-default-build-as-user-job-04] | | `-- Extracting gettext-runtime-0.22.3: .......... done [140amd64-default-build-as-user-job-04] | | `-- Installing zstd-1.5.5... [140amd64-default-build-as-user-job-04] | | `-- Installing liblz4-1.9.4,1... [140amd64-default-build-as-user-job-04] | | `-- Extracting liblz4-1.9.4,1: .......... done [140amd64-default-build-as-user-job-04] | | `-- Extracting zstd-1.5.5: .......... done [140amd64-default-build-as-user-job-04] | `-- Extracting binutils-2.40_4,1: .......... done [140amd64-default-build-as-user-job-04] | `-- Installing gmp-6.3.0... [140amd64-default-build-as-user-job-04] | `-- Extracting gmp-6.3.0: .......... done [140amd64-default-build-as-user-job-04] | `-- Installing mpc-1.3.1_1... [140amd64-default-build-as-user-job-04] | | `-- Installing mpfr-4.2.1,1... [140amd64-default-build-as-user-job-04] | | `-- Extracting mpfr-4.2.1,1: .......... done [140amd64-default-build-as-user-job-04] | `-- Extracting mpc-1.3.1_1: ......... done [140amd64-default-build-as-user-job-04] `-- Extracting gcc12-12.2.0_7: .......... done [140amd64-default-build-as-user-job-04] `-- Installing gsl-2.7.1... [140amd64-default-build-as-user-job-04] `-- Extracting gsl-2.7.1: .......... done [140amd64-default-build-as-user-job-04] `-- Installing lapack-3.11.0_1... [140amd64-default-build-as-user-job-04] | `-- Installing blas-3.11.0_1... [140amd64-default-build-as-user-job-04] | `-- Extracting blas-3.11.0_1: ........ done [140amd64-default-build-as-user-job-04] `-- Extracting lapack-3.11.0_1: .......... done [140amd64-default-build-as-user-job-04] `-- Installing libICE-1.1.0_2,1... [140amd64-default-build-as-user-job-04] `-- Extracting libICE-1.1.0_2,1: .......... done [140amd64-default-build-as-user-job-04] `-- Installing libX11-1.8.7,1... [140amd64-default-build-as-user-job-04] | `-- Installing libxcb-1.15_1... [140amd64-default-build-as-user-job-04] | | `-- Installing libXau-1.0.9... <snip> 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... freebsd14.0 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... (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 =========================================================================== =======================<phase: build >============================ ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for locarna-2.0.0 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0' Making all in src gmake[2]: 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 -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 -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 -MT LocARNA/aligner_n.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/aligner_n.lo LocARNA/aligner_n.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/aligner_n.lo -MD -MP -MF LocARNA/.deps/aligner_n.Tpo -c LocARNA/aligner_n.cc -fPIC -DPIC -o LocARNA/.libs/aligner_n.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/aligner.lo -MD -MP -MF LocARNA/.deps/aligner.Tpo -c LocARNA/aligner.cc -fPIC -DPIC -o LocARNA/.libs/aligner.o depbase=`echo LocARNA/alignment.lo | sed 's|[^/]*$|.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 -MT LocARNA/alignment.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/alignment.lo LocARNA/alignment.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/alignment.lo -MD -MP -MF LocARNA/.deps/alignment.Tpo -c LocARNA/alignment.cc -fPIC -DPIC -o LocARNA/.libs/alignment.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/aligner_n.lo -MD -MP -MF LocARNA/.deps/aligner_n.Tpo -c LocARNA/aligner_n.cc -o LocARNA/aligner_n.o >/dev/null 2>&1 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/aligner.lo -MD -MP -MF LocARNA/.deps/aligner.Tpo -c LocARNA/aligner.cc -o LocARNA/aligner.o >/dev/null 2>&1 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/alignment.lo -MD -MP -MF LocARNA/.deps/alignment.Tpo -c LocARNA/alignment.cc -o LocARNA/alignment.o >/dev/null 2>&1 depbase=`echo LocARNA/anchor_constraints.lo | sed 's|[^/]*$|.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 -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 -MT LocARNA/arc_matches.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/arc_matches.lo LocARNA/arc_matches.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/anchor_constraints.lo -MD -MP -MF LocARNA/.deps/anchor_constraints.Tpo -c LocARNA/anchor_constraints.cc -fPIC -DPIC -o LocARNA/.libs/anchor_constraints.o depbase=`echo LocARNA/aux.lo | sed 's|[^/]*$|.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 -MT LocARNA/aux.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/aux.lo LocARNA/aux.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 -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 -MT LocARNA/aux.lo -MD -MP -MF LocARNA/.deps/aux.Tpo -c LocARNA/aux.cc -fPIC -DPIC -o LocARNA/.libs/aux.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 -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 -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 -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 depbase=`echo 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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 -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 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 -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 depbase=`echo LocARNA/multiple_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 -MT 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LocARNA/ribosum.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 -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 -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 -MT LocARNA/ribosum.lo -MD -MP -MF LocARNA/.deps/ribosum.Tpo -c LocARNA/ribosum.cc -o LocARNA/ribosum.o >/dev/null 2>&1 depbase=`echo 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/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 -MT LocARNA/scoring.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/scoring.lo LocARNA/scoring.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/scoring.lo -MD -MP -MF LocARNA/.deps/scoring.Tpo -c LocARNA/scoring.cc -fPIC -DPIC -o LocARNA/.libs/scoring.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/rna_data.lo -MD -MP -MF LocARNA/.deps/rna_data.Tpo -c LocARNA/rna_data.cc -o LocARNA/rna_data.o >/dev/null 2>&1 depbase=`echo LocARNA/sequence.lo | sed 's|[^/]*$|.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 -MT LocARNA/sequence.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/sequence.lo LocARNA/sequence.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 -MT LocARNA/sequence.lo -MD -MP -MF LocARNA/.deps/sequence.Tpo -c LocARNA/sequence.cc -fPIC -DPIC -o LocARNA/.libs/sequence.o LocARNA/scoring.cc:57:29: error: no member named 'bind2nd' in namespace 'std' std::bind2nd(std::minus<score_t>(), x)); ~~~~~^ LocARNA/scoring.cc:61:26: error: no member named 'bind2nd' in namespace 'std' m.transform(std::bind2nd(std::minus<score_t>(), x)); ~~~~~^ 2 errors generated. gmake[2]: *** [Makefile:939: LocARNA/scoring.lo] Error 1 gmake[2]: *** Waiting for unfinished jobs.... 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 -MT LocARNA/sequence.lo -MD -MP -MF LocARNA/.deps/sequence.Tpo -c LocARNA/sequence.cc -o LocARNA/sequence.o >/dev/null 2>&1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0/src' gmake[1]: *** [Makefile:671: all-recursive] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/locarna/work/locarna-2.0.0' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/locarna