From nobody Tue Nov 07 23:46:34 2023 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4SQ4cW1l5zz4yjmQ for ; Tue, 7 Nov 2023 23:46:35 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4SQ4cV48vdz3JMr for ; Tue, 7 Nov 2023 23:46:34 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1699400794; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=VS0RkdDR6/zhjTt8E+jZkwxQwTMVI4HuWJuVucgDdqg=; b=C8slQKGvosuOujRGzL81GbD7+lwS3N7lSsg1vDafTRRYDSrfVkNzaedB1F9cuNG9FLYHWC GhRaNrrQYBTyFRBZhh8MyWRLUXG2ZyfLZOwijhi/vU92fs9Uh3aTuIMcRU0ja2D/EFNiwm BI69fg1N91lmiV4ikb5mOzpBm5BjgHw9SEOLwQNxaNYhe8YRRplEx+hPQBjPlwhCnuXHYb orRt9ccz/4dvpAU+xI6KFp1t/9NlDSYABoPGlSRjb/52QA9oxkVVg+pRnGACqIN/tvN7BR YpP6uupw9q2nm5qtynvraqwTzAEabr7E8MOHfS2BwwFBeg7ttYcC3wzAgppKsg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1699400794; a=rsa-sha256; cv=none; b=Hi+yhvmjfazcC3O77gyXzHv/Z/We5BdZCOhwNXY2crTYRbnqFKpjoLfWfUGgQXjQdPDJHz VB15aL+SMcvhF+VTXl6ZLK5mC4Ue+LEfF6TzPs0wL3NzjdZFWQgfgr9vGqoku9xfrO4CeQ MkOJdB02jyTsLKVgN2CoduUqV2y0RAJC2Bq/XSDtwdcy1U+euZKshLMJ2LFD5ed4h3ZDw6 jc/Xm4w6/27g+ERsLSl5sA7YvXnUJH6e2nkwEiihzels1V75Tfv6t7EuSF/+pBajdJNGyh bFYcWe1ST/aRf73GE2dOGR9S43V5yxe2j3ABg6cGAUXAJKfnc7zqtHYXqlzJcA== Received: from beefy17.nyi.freebsd.org (beefy17.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:20]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4SQ4cV3CVQz18sL for ; Tue, 7 Nov 2023 23:46:34 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 7e65 by beefy17.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy17.nyi.freebsd.org); Tue, 07 Nov 2023 23:46:34 +0000 To: yuri@FreeBSD.org Subject: [package - main-i386-default][biology/locarna] Failed for locarna-2.0.0 in build Cc: pkg-fallout@FreeBSD.org Date: Tue, 07 Nov 2023 23:46:34 +0000 Message-Id: <654acc5a.7e65.47b47ba@beefy17.nyi.freebsd.org> From: List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org 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/beefy17/data/main-i386-default/pd5268d5f7157_s501bdf3001/logs/locarna-2.0.0.log Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=pd5268d5f7157_s501bdf3001 Log: =>> Building biology/locarna build started at Tue Nov 7 23:44:50 UTC 2023 port directory: /usr/ports/biology/locarna package name: locarna-2.0.0 building for: FreeBSD main-i386-default-job-01 15.0-CURRENT FreeBSD 15.0-CURRENT 1500003 i386 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1014 Jul 18 01:01 /usr/ports/biology/locarna/Makefile Ports top last git commit: d5268d5f715 Ports top unclean checkout: no Port dir last git commit: 2ce2ca5b614 Port dir unclean checkout: no Poudriere version: poudriere-git-3.3.0-1251-ge8a0e12e Host OSVERSION: 1500000 Jail OSVERSION: 1500003 Job Id: 01 !!! Jail is newer than host. (Jail: 1500003, Host: 1500000) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 OSVERSION=1500003 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin UNAME_m=i386 UNAME_p=i386 UNAME_r=15.0-CURRENT LOCALBASE=/usr/local UNAME_v=FreeBSD 15.0-CURRENT 1500003 USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.3.0-1251-ge8a0e12e MASTERMNT=/usr/local/poudriere/data/.m/main-i386-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/main-i386-default/01/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-i386-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-i386-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.3.0-1251-ge8a0e12e 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=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.36.1 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 PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 524288 stack size (kbytes, -s) 65536 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===== 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-1.20.8.pkg [main-i386-default-job-01] Installing pkg-1.20.8... [main-i386-default-job-01] Extracting pkg-1.20.8: .......... done ===> locarna-2.0.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of locarna-2.0.0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== 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 =========================================================================== =================================================== ===== 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. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== 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 ===> Extracting for locarna-2.0.0 => 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 =========================================================================== =================================================== ===== 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 [main-i386-default-job-01] Installing viennarna-2.6.4... [main-i386-default-job-01] `-- Installing gcc12-12.2.0_6... [main-i386-default-job-01] | `-- Installing binutils-2.40_4,1... [main-i386-default-job-01] | | `-- Installing gettext-runtime-0.22.3... [main-i386-default-job-01] | | `-- Installing indexinfo-0.3.1... [main-i386-default-job-01] | | `-- Extracting indexinfo-0.3.1: .... done [main-i386-default-job-01] | | `-- Extracting gettext-runtime-0.22.3: .......... done [main-i386-default-job-01] | | `-- Installing zstd-1.5.5... [main-i386-default-job-01] | | `-- Installing liblz4-1.9.4,1... [main-i386-default-job-01] | | `-- Extracting liblz4-1.9.4,1: .......... done [main-i386-default-job-01] | | `-- Extracting zstd-1.5.5: .......... done 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... freebsd15.0 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 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/aligner.lo -MD -MP -MF LocARNA/.deps/aligner.Tpo -c LocARNA/aligner.cc -fPIC -DPIC -o LocARNA/.libs/aligner.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/aligner_n.lo -MD -MP -MF LocARNA/.deps/aligner_n.Tpo -c LocARNA/aligner_n.cc -fPIC -DPIC -o LocARNA/.libs/aligner_n.o depbase=`echo LocARNA/alignment.lo | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/alignment.lo -MD -MP -MF LocARNA/.deps/alignment.Tpo -c LocARNA/alignment.cc -fPIC -DPIC -o LocARNA/.libs/alignment.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/aligner.lo -MD -MP -MF LocARNA/.deps/aligner.Tpo -c LocARNA/aligner.cc -o LocARNA/aligner.o >/dev/null 2>&1 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/alignment.lo -MD -MP -MF LocARNA/.deps/alignment.Tpo -c LocARNA/alignment.cc -o LocARNA/alignment.o >/dev/null 2>&1 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/aligner_n.lo -MD -MP -MF LocARNA/.deps/aligner_n.Tpo -c LocARNA/aligner_n.cc -o LocARNA/aligner_n.o >/dev/null 2>&1 depbase=`echo LocARNA/anchor_constraints.lo | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/anchor_constraints.lo -MD -MP -MF LocARNA/.deps/anchor_constraints.Tpo -c LocARNA/anchor_constraints.cc -fPIC -DPIC -o LocARNA/.libs/anchor_constraints.o depbase=`echo LocARNA/arc_matches.lo | sed 's|[^/]*$|.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 $depbase.Plo libtool: compile: c++ 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LocARNA/rna_ensemble.lo -MD -MP -MF LocARNA/.deps/rna_ensemble.Tpo -c LocARNA/rna_ensemble.cc -fPIC -DPIC -o LocARNA/.libs/rna_ensemble.o libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/rna_ensemble.lo -MD -MP -MF LocARNA/.deps/rna_ensemble.Tpo -c LocARNA/rna_ensemble.cc -o LocARNA/rna_ensemble.o >/dev/null 2>&1 libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/ribosum.lo -MD -MP -MF LocARNA/.deps/ribosum.Tpo -c LocARNA/ribosum.cc -o LocARNA/ribosum.o >/dev/null 2>&1 depbase=`echo LocARNA/rna_structure.lo | sed 's|[^/]*$|.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/rna_structure.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/rna_structure.lo LocARNA/rna_structure.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/catch2 -MT LocARNA/rna_structure.lo -MD -MP -MF LocARNA/.deps/rna_structure.Tpo -c LocARNA/rna_structure.cc -fPIC -DPIC -o LocARNA/.libs/rna_structure.o depbase=`echo LocARNA/scoring.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I/usr/local/include -I/usr/local/include/ViennaRNA -pthread -O2 -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_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 -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 LocARNA/scoring.cc:57:29: error: no member named 'bind2nd' in namespace 'std' std::bind2nd(std::minus(), x)); ~~~~~^ LocARNA/scoring.cc:61:26: error: no member named 'bind2nd' in namespace 'std' m.transform(std::bind2nd(std::minus(), x)); ~~~~~^ 2 errors generated. gmake[2]: *** [Makefile:939: LocARNA/scoring.lo] Error 1 gmake[2]: *** Waiting for unfinished jobs.... 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