From owner-freebsd-pkg-fallout@freebsd.org Sun Aug 23 09:08:51 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 4466C3B6EFC for ; Sun, 23 Aug 2020 09:08:51 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.nyi.freebsd.org (mailman.nyi.freebsd.org [IPv6:2610:1c1:1:606c::50:13]) by mx1.freebsd.org (Postfix) with ESMTP id 4BZ8ZC1LPBz4S83 for ; Sun, 23 Aug 2020 09:08:51 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id 2DF023B6EFB; Sun, 23 Aug 2020 09:08:51 +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 2D9F93B730C for ; Sun, 23 Aug 2020 09:08:51 +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 4BZ8ZB70J6z4S2x; Sun, 23 Aug 2020 09:08:50 +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 D081224D9C; Sun, 23 Aug 2020 09:08:50 +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 07N98oIX020246; Sun, 23 Aug 2020 09:08:50 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy18.nyi.freebsd.org (8.15.2/8.15.2/Submit) id 07N98oc0020244; Sun, 23 Aug 2020 09:08:50 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sun, 23 Aug 2020 09:08:50 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202008230908.07N98oc0020244@beefy18.nyi.freebsd.org> To: yuri@FreeBSD.org Subject: [package - head-amd64-default][science/apbs] Failed for apbs-1.5.102 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: Sun, 23 Aug 2020 09:08:51 -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: yuri@FreeBSD.org Ident: $FreeBSD: head/science/apbs/Makefile 500699 2019-05-03 06:15:44Z yuri $ Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p545731_s364466/logs/apbs-1.5.102.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p545731_s364466 Log: =>> Building science/apbs build started at Sun Aug 23 09:08:24 UTC 2020 port directory: /usr/ports/science/apbs package name: apbs-1.5.102 building for: FreeBSD head-amd64-default-job-06 13.0-CURRENT FreeBSD 13.0-CURRENT 1300110 amd64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/science/apbs/Makefile 500699 2019-05-03 06:15:44Z yuri $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300100 Jail OSVERSION: 1300110 Job Id: 06 !!! Jail is newer than host. (Jail: 1300110, Host: 1300100) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300110 UNAME_v=FreeBSD 13.0-CURRENT 1300110 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--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/apbs/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/apbs/work HOME=/wrkdirs/usr/ports/science/apbs/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/apbs/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/apbs/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/apbs/work HOME=/wrkdirs/usr/ports/science/apbs/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/apbs/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 DESTDIR=/wrkdirs/usr/ports/science/apbs/work/stage 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 " 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-- CMAKE_BUILD_TYPE="release" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/apbs" EXAMPLESDIR="share/examples/apbs" DATADIR="share/apbs" WWWDIR="www/apbs" ETCDIR="etc/apbs" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/apbs DOCSDIR=/usr/local/share/doc/apbs EXAMPLESDIR=/usr/local/share/examples/apbs WWWDIR=/usr/local/www/apbs ETCDIR=/usr/local/etc/apbs --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-rc1-47-gff47911ddfc) 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-rc1-47-gff47911ddfc) 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-rc1-47-gff47911ddfc) 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=1300110 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 MIT accepted by the user =========================================================================== =================================================== ===> apbs-1.5.102 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.14.7.txz [head-amd64-default-job-06] Installing pkg-1.14.7... [head-amd64-default-job-06] Extracting pkg-1.14.7: .......... done ===> apbs-1.5.102 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of apbs-1.5.102 =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by apbs-1.5.102 for building =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by apbs-1.5.102 for building => SHA256 Checksum OK for Electrostatics-apbs-pdb2pqr-apbs-1.5-102-g500c1473_GH0.tar.gz. => SHA256 Checksum OK for Electrostatics-FETK-0c6fdea_GH0.tar.gz. => SHA256 Checksum OK for Electrostatics-geoflow_c-e8ce510_GH0.tar.gz. => SHA256 Checksum OK for lwwilson1-TABIPB-7e3a407_GH0.tar.gz. => SHA256 Checksum OK for lwwilson1-mesh_routines-ddb75cb_GH0.tar.gz. => SHA256 Checksum OK for davas301-pb_solvers-4858465_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by apbs-1.5.102 for building ===> Extracting for apbs-1.5.102 => SHA256 Checksum OK for Electrostatics-apbs-pdb2pqr-apbs-1.5-102-g500c1473_GH0.tar.gz. => SHA256 Checksum OK for Electrostatics-FETK-0c6fdea_GH0.tar.gz. => SHA256 Checksum OK for Electrostatics-geoflow_c-e8ce510_GH0.tar.gz. => SHA256 Checksum OK for lwwilson1-TABIPB-7e3a407_GH0.tar.gz. => SHA256 Checksum OK for lwwilson1-mesh_routines-ddb75cb_GH0.tar.gz. => SHA256 Checksum OK for davas301-pb_solvers-4858465_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for apbs-1.5.102 =========================================================================== =================================================== ===> apbs-1.5.102 depends on file: /usr/local/bin/cmake - not found -- Build files have been written to: /wrkdirs/usr/ports/science/apbs/work/.build =========================================================================== =================================================== ===> Building for apbs-1.5.102 [1/102] /usr/bin/cc -Dmaloc_EXPORTS -I/usr/local/include -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/base -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/psh -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/vsh -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/vsys -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -g -DNDEBUG -fPIC -MD -MT externals/fetk/maloc/src/CMakeFiles/maloc.dir/base/maloc_base.c.o -MF externals/fetk/maloc/src/CMakeFiles/maloc.dir/base/maloc_base.c.o.d -o externals/fetk/maloc/src/CMakeFiles/maloc.dir/base/maloc_base.c.o -c /wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/sr c/base/maloc_base.c [2/102] /usr/bin/cc -Dmaloc_EXPORTS -I/usr/local/include -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/base -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/psh -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/vsh -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/vsys -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -g -DNDEBUG -fPIC -MD -MT externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/psh.c.o -MF externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/psh.c.o.d -o externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/psh.c.o -c /wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/psh/psh.c [3/102] /usr/bin/cc -Dmaloc_EXPORTS -I/usr/local/include -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/base -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/psh -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/vsh -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/vsys -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -g -DNDEBUG -fPIC -MD -MT externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vcom.c.o -MF externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vcom.c.o.d -o externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vcom.c.o -c /wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/psh/vcom.c [4/102] /usr/bin/cc -Dmaloc_EXPORTS -I/usr/local/include -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/base -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/psh -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/vsh -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/vsys -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -g -DNDEBUG -fPIC -MD -MT externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vmp.c.o -MF externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vmp.c.o.d -o externals/fetk/maloc/src/CMakeFiles/maloc.dir/psh/vmp.c.o -c /wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/psh/vmp.c [5/102] /usr/bin/cc -Dmaloc_EXPORTS -I/usr/local/include 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-I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/vsh -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/psh -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src -Isrc -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -g -DNDEBUG -fPIC -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -c /wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mgfasd.c [61/102] : && /usr/bin/cc -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -g -DNDEBUG -fstack-protector-strong -shared -Wl,-soname,libapbs_pmgc.so -o lib/libapbs_pmgc.so src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfas d.c.o -L/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/lib -Wl,-rpath,/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/lib: -lm -lstdc++ /wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/lib/libmaloc.so && : FAILED: lib/libapbs_pmgc.so : && /usr/bin/cc -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -g -DNDEBUG -fstack-protector-strong -shared -Wl,-soname,libapbs_pmgc.so -o lib/libapbs_pmgc.so src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -L/ wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/lib -Wl,-rpath,/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/lib: -lm -lstdc++ /wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/lib/libmaloc.so && : ld: error: duplicate symbol: charge >>> defined at mypdec.h:72 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:72) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(charge) >>> defined at mypdec.h:72 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:72) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o:(.bss+0x50) ld: error: duplicate symbol: conc1 >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(conc1) >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o:(.bss+0x18) ld: error: duplicate symbol: conc2 >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(conc2) >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o:(.bss+0x20) ld: error: duplicate symbol: conc3 >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(conc3) >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o:(.bss+0x28) ld: error: duplicate symbol: nion >>> defined at mypdec.h:71 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:71) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(nion) >>> defined at mypdec.h:71 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:71) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o:(.bss+0x40) ld: error: duplicate symbol: relSize >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(relSize) >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o:(.bss+0x38) ld: error: duplicate symbol: sconc >>> defined at mypdec.h:73 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:73) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(sconc) >>> defined at mypdec.h:73 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:73) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o:(.bss+0x1E0) ld: error: duplicate symbol: v1 >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(v1) >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o:(.bss+0x0) ld: error: duplicate symbol: v2 >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(v2) >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o:(.bss+0x8) ld: error: duplicate symbol: v3 >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(v3) >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o:(.bss+0x10) ld: error: duplicate symbol: vol >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(vol) >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o:(.bss+0x30) ld: error: duplicate symbol: charge >>> defined at mypdec.h:72 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:72) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(charge) >>> defined at mypdec.h:72 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:72) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o:(.bss+0x50) ld: error: duplicate symbol: conc1 >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(conc1) >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o:(.bss+0x18) ld: error: duplicate symbol: conc2 >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(conc2) >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o:(.bss+0x20) ld: error: duplicate symbol: conc3 >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(conc3) >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o:(.bss+0x28) ld: error: duplicate symbol: nion >>> defined at mypdec.h:71 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:71) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(nion) >>> defined at mypdec.h:71 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:71) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o:(.bss+0x40) ld: error: duplicate symbol: relSize >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(relSize) >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o:(.bss+0x38) ld: error: duplicate symbol: sconc >>> defined at mypdec.h:73 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:73) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(sconc) >>> defined at mypdec.h:73 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:73) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o:(.bss+0x1E0) ld: error: duplicate symbol: v1 >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(v1) >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o:(.bss+0x0) ld: error: duplicate symbol: v2 >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o:(v2) >>> defined at mypdec.h:70 (/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/pmgc/mypdec.h:70) >>> src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o:(.bss+0x8) ld: error: too many errors emitted, stopping now (use -error-limit=0 to see all errors) cc: error: linker command failed with exit code 1 (use -v to see invocation) [62/102] /usr/bin/cc -Dapbs_mg_EXPORTS -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/base -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/vsys -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/vsh -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/fetk/maloc/src/psh -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src -Isrc -I/wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -g -DNDEBUG -fPIC -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o -MF src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o.d -o src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o -c /wrkdirs/usr/ports/science/apbs/work/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/src/mg/vgrid.c ninja: build stopped: subcommand failed. ===> 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/science/apbs