From owner-freebsd-pkg-fallout@freebsd.org Sat Sep 5 04:32:19 2020 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id C99FF3DE5B1 for ; Sat, 5 Sep 2020 04:32:19 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.nyi.freebsd.org (unknown [127.0.1.3]) by mx1.freebsd.org (Postfix) with ESMTP id 4Bk1q74wWZz3cRX for ; Sat, 5 Sep 2020 04:32:19 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id A8E8A3DE5B0; Sat, 5 Sep 2020 04:32:19 +0000 (UTC) Delivered-To: pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id A8AB53DE639 for ; Sat, 5 Sep 2020 04:32:19 +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 "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4Bk1q74CMWz3cP0; Sat, 5 Sep 2020 04:32:19 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy18.nyi.freebsd.org (beefy18.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:f3]) (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 did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 73DD5182B3; Sat, 5 Sep 2020 04:32:19 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy18.nyi.freebsd.org (localhost [127.0.0.1]) by beefy18.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id 0854WJKL009299; Sat, 5 Sep 2020 04:32:19 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy18.nyi.freebsd.org (8.15.2/8.15.2/Submit) id 0854WJVn009298; Sat, 5 Sep 2020 04:32:19 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sat, 5 Sep 2020 04:32:19 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202009050432.0854WJVn009298@beefy18.nyi.freebsd.org> To: yuri@FreeBSD.org Subject: [package - head-amd64-default][biology/viennarna] Failed for viennarna-2.4.14_1 in build Cc: pkg-fallout@FreeBSD.org X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.33 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 05 Sep 2020 04:32:19 -0000 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 Last committer: dinoex@FreeBSD.org Ident: $FreeBSD: head/biology/viennarna/Makefile 533989 2020-05-04 21:31:39Z dinoex $ Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p547580_s365355/logs/viennarna-2.4.14_1.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p547580_s365355 Log: =>> Building biology/viennarna build started at Sat Sep 5 04:27:24 UTC 2020 port directory: /usr/ports/biology/viennarna package name: viennarna-2.4.14_1 building for: FreeBSD head-amd64-default-job-12 13.0-CURRENT FreeBSD 13.0-CURRENT 1300113 amd64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/biology/viennarna/Makefile 533989 2020-05-04 21:31:39Z dinoex $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300100 Jail OSVERSION: 1300113 Job Id: 12 !!! Jail is newer than host. (Jail: 1300113, Host: 1300100) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300113 UNAME_v=FreeBSD 13.0-CURRENT 1300113 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for viennarna-2.4.14_1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --enable-shared --disable-static --with-gsl --with-cluster --with-kinwalker --enable-mpfr --without-python --without-python3 --without-perl --x-libraries=/usr/local/lib --x-includes=/usr/local/include --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/viennarna/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/viennarna/work HOME=/wrkdirs/usr/ports/biology/viennarna/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/viennarna/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/usr/local/bin/bash CONFIG_SHELL=/usr/local/bin/bash CMAKE_PREFIX_PATH="/usr/local" 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/viennarna/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/viennarna/work HOME=/wrkdirs/usr/ports/biology/viennarna/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/viennarna/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" 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-- PORTDOCS="" PORTEXAMPLES="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.0 PERL_VER=5.32 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/5.32 DOCSDIR="share/doc/ViennaRNA" EXAMPLESDIR="share/examples/ViennaRNA" DATADIR="share/viennarna" WWWDIR="www/viennarna" ETCDIR="etc/viennarna" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/viennarna DOCSDIR=/usr/local/share/doc/ViennaRNA EXAMPLESDIR=/usr/local/share/examples/ViennaRNA WWWDIR=/usr/local/www/viennarna ETCDIR=/usr/local/etc/viennarna --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 #### /usr/local/etc/poudriere.d/make.conf #### # 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 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc2-0-g414f32a9e86) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc2-0-g414f32a9e86) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc2-0-g414f32a9e86) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300113 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 1024 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-- =================================================== ===> License ViennaRNALicense accepted by the user =========================================================================== =================================================== ===> viennarna-2.4.14_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.14.7.txz [head-amd64-default-job-12] Installing pkg-1.14.7... [head-amd64-default-job-12] Extracting pkg-1.14.7: .......... done ===> viennarna-2.4.14_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of viennarna-2.4.14_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License ViennaRNALicense accepted by the user ===> Fetching all distfiles required by viennarna-2.4.14_1 for building =========================================================================== =================================================== ===> License ViennaRNALicense accepted by the user ===> Fetching all distfiles required by viennarna-2.4.14_1 for building => SHA256 Checksum OK for ViennaRNA-2.4.14.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License ViennaRNALicense accepted by the user ===> Fetching all distfiles required by viennarna-2.4.14_1 for building ===> Extracting for viennarna-2.4.14_1 => SHA256 Checksum OK for ViennaRNA-2.4.14.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for viennarna-2.4.14_1 ===> Applying FreeBSD patches for viennarna-2.4.14_1 from /usr/ports/biology/viennarna/files =========================================================================== =================================================== ===> viennarna-2.4.14_1 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.0.18_3.txz [head-amd64-default-job-12] Installing bash-5.0.18_3... [head-amd64-default-job-12] `-- Installing gettext-runtime-0.21... [head-amd64-default-job-12] | `-- Installing indexinfo-0.3.1... [head-amd64-default-job-12] | `-- Extracting indexinfo-0.3.1: .... done depbase=`echo treeplot.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT treeplot.o -MD -MP -MF $depbase.Tpo -c -o treeplot.o treeplot.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo AD_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT AD_main.o -MD -MP -MF $depbase.Tpo -c -o AD_main.o AD_main.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo statgeom.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT statgeom.o -MD -MP -MF $depbase.Tpo -c -o statgeom.o statgeom.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo AS_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT AS_main.o -MD -MP -MF $depbase.Tpo -c -o AS_main.o AS_main.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo PS3D.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT PS3D.o -MD -MP -MF $depbase.Tpo -c -o PS3D.o PS3D.c &&\ mv -f $depbase.Tpo $depbase.Po /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -fstack-protector-strong -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o ../../src/ViennaRNA/libRNA_conv.la -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -fstack-protector-strong -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o ../../src/ViennaRNA/libRNA_conv.la -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -fstack-protector-strong -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -fstack-protector-strong -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib -lgsl -lgslcblas -lm -pthread -fopenmp gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Cluster' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src' gmake[4]: Nothing to be done for 'all-am'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src' Making all in man gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/man' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/man' Making all in misc gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/misc' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/misc' Making all in doc gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/doc' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/doc' Making all in RNA-Tutorial gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/RNA-Tutorial' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/RNA-Tutorial' Making all in interfaces gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/interfaces' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/interfaces' gmake[4]: Nothing to be done for 'all-am'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/interfaces' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/interfaces' Making all in src/Kinfold gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold' gmake all-recursive gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold' Making all in Example gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold/Example' gmake[5]: Nothing to be done for 'all'. gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold/Example' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold' cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT baum.o -MD -MP -MF .deps/baum.Tpo -c -o baum.o baum.c cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cache.o -MD -MP -MF .deps/cache.Tpo -c -o cache.o cache.c mv -f .deps/cache.Tpo .deps/cache.Po cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT globals.o -MD -MP -MF .deps/globals.Tpo -c -o globals.o globals.c globals.c:333:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else GTV.seed = 1; ^ globals.c:348:9: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat] &GAV.phi_bounds[0], ^~~~~~~~~~~~~~~~~~ globals.c:349:9: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat] &GAV.phi_bounds[1], ^~~~~~~~~~~~~~~~~~ globals.c:350:9: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat] &GAV.phi_bounds[2]) == 0) ^~~~~~~~~~~~~~~~~~ globals.c:437:8: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat] &GAV.phi_bounds[0], ^~~~~~~~~~~~~~~~~~ globals.c:438:8: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat] &GAV.phi_bounds[1], ^~~~~~~~~~~~~~~~~~ globals.c:439:8: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat] &GAV.phi_bounds[2]) == 0) ^~~~~~~~~~~~~~~~~~ 7 warnings generated. mv -f .deps/globals.Tpo .deps/globals.Po cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c main.c:175:8: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (c=strchr(ctmp, '&')) { ~^~~~~~~~~~~~~~~~~~ main.c:175:8: note: place parentheses around the assignment to silence this warning if (c=strchr(ctmp, '&')) { ^ ( ) main.c:175:8: note: use '==' to turn this assignment into an equality comparison if (c=strchr(ctmp, '&')) { ^ == main.c:200:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (c=strchr(GAV.startform, '&')) { ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ main.c:200:10: note: place parentheses around the assignment to silence this warning if (c=strchr(GAV.startform, '&')) { ^ ( ) main.c:200:10: note: use '==' to turn this assignment into an equality comparison if (c=strchr(GAV.startform, '&')) { ^ == main.c:224:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if (c=strchr(ctmp, '&')) { ~^~~~~~~~~~~~~~~~~~ main.c:224:12: note: place parentheses around the assignment to silence this warning if (c=strchr(ctmp, '&')) { ^ ( ) main.c:224:12: note: use '==' to turn this assignment into an equality comparison if (c=strchr(ctmp, '&')) { ^ == 3 warnings generated. mv -f .deps/main.Tpo .deps/main.Po cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT nachbar.o -MD -MP -MF .deps/nachbar.Tpo -c -o nachbar.o nachbar.c nachbar.c:311:43: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat] sprintf(format, "%%-%ds %%6.2f %%10.3f", strlen(GAV.farbe_full)+1); ~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %lu 1 warning generated. mv -f .deps/nachbar.Tpo .deps/nachbar.Po cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cmdline.o -MD -MP -MF .deps/cmdline.Tpo -c -o cmdline.o cmdline.c mv -f .deps/baum.Tpo .deps/baum.Po mv -f .deps/cmdline.Tpo .deps/cmdline.Po cc -I./../../src/ViennaRNA -I./../../src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fstack-protector-strong -o Kinfold baum.o cache.o globals.o main.o nachbar.o cmdline.o -fno-strict-aliasing -L./../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lmpfr -lgmp -lm -L/usr/local/lib ld: error: duplicate symbol: GAV >>> defined at baum.c >>> baum.o:(GAV) >>> defined at globals.c >>> globals.o:(.bss+0x0) ld: error: duplicate symbol: GSV >>> defined at baum.c >>> baum.o:(GSV) >>> defined at globals.c >>> globals.o:(.bss+0x860) ld: error: duplicate symbol: GTV >>> defined at baum.c >>> baum.o:(GTV) >>> defined at globals.c >>> globals.o:(.bss+0x8B0) ld: error: duplicate symbol: GAV >>> defined at baum.c >>> baum.o:(GAV) >>> defined at main.c >>> main.o:(.bss+0x0) ld: error: duplicate symbol: GSV >>> defined at baum.c >>> baum.o:(GSV) >>> defined at main.c >>> main.o:(.bss+0x860) ld: error: duplicate symbol: GTV >>> defined at baum.c >>> baum.o:(GTV) >>> defined at main.c >>> main.o:(.bss+0x8B0) ld: error: duplicate symbol: GAV >>> defined at baum.c >>> baum.o:(GAV) >>> defined at nachbar.c >>> nachbar.o:(.bss+0x18) ld: error: duplicate symbol: GSV >>> defined at baum.c >>> baum.o:(GSV) >>> defined at nachbar.c >>> nachbar.o:(.bss+0x888) ld: error: duplicate symbol: GTV >>> defined at baum.c >>> baum.o:(GTV) >>> defined at nachbar.c >>> nachbar.o:(.bss+0x8E8) cc: error: linker command failed with exit code 1 (use -v to see invocation) gmake[5]: *** [Makefile:486: Kinfold] Error 1 gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold' gmake[4]: *** [Makefile:571: all-recursive] Error 1 gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold' gmake[3]: *** [Makefile:389: all] Error 2 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14/src/Kinfold' gmake[2]: *** [Makefile:668: all-recursive] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14' gmake[1]: *** [Makefile:561: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.4.14' ===> 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/viennarna