From owner-freebsd-pkg-fallout@freebsd.org Sat Mar 17 23:19:04 2018 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 75ED5F4D9E5 for ; Sat, 17 Mar 2018 23:19:04 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.ysv.freebsd.org (mailman.ysv.freebsd.org [IPv6:2001:1900:2254:206a::50:5]) by mx1.freebsd.org (Postfix) with ESMTP id D1C64730FC for ; Sat, 17 Mar 2018 23:19:03 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id 887BBF4D9DF; Sat, 17 Mar 2018 23:19:03 +0000 (UTC) Delivered-To: pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 52FB2F4D9DE for ; Sat, 17 Mar 2018 23:19:03 +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 TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 02E5D730FA for ; Sat, 17 Mar 2018 23:19:03 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from thunderx1.nyi.freebsd.org (thunderx1.nyi.freebsd.org [IPv6:2610:1c1:1:6082::16:fb]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id D360C189E6 for ; Sat, 17 Mar 2018 23:19:02 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from thunderx1.nyi.freebsd.org (localhost [127.0.0.1]) by thunderx1.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id w2HNJ2KC047884 for ; Sat, 17 Mar 2018 23:19:02 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by thunderx1.nyi.freebsd.org (8.15.2/8.15.2/Submit) id w2HNJ20J047882; Sat, 17 Mar 2018 23:19:02 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sat, 17 Mar 2018 23:19:02 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201803172319.w2HNJ20J047882@thunderx1.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 111arm64-quarterly][biology/canu] Failed for canu-1.6 in build X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.25 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 17 Mar 2018 23:19:04 -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: jwb@FreeBSD.org Last committer: jwb@FreeBSD.org Ident: $FreeBSD: branches/2018Q1/biology/canu/Makefile 456982 2017-12-22 14:14:11Z jwb $ Log URL: http://thunderx1.nyi.freebsd.org/data/111arm64-quarterly/464745/logs/canu-1.6.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=111arm64-quarterly&build=464745 Log: =>> Building biology/canu build started at Sat Mar 17 23:18:04 UTC 2018 port directory: /usr/ports/biology/canu package name: canu-1.6 building for: FreeBSD 111arm64-quarterly-job-20 11.1-RELEASE FreeBSD 11.1-RELEASE arm64 maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: branches/2018Q1/biology/canu/Makefile 456982 2017-12-22 14:14:11Z jwb $ Poudriere version: 3.2.5-24-gdf5c0606 Host OSVERSION: 1200060 Jail OSVERSION: 1101001 Job Id: 20 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1101001 UNAME_v=FreeBSD 11.1-RELEASE UNAME_r=11.1-RELEASE 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=3.2.5-24-gdf5c0606 MASTERMNT=/usr/local/poudriere/data/.m/111arm64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/111arm64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=111arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/111arm64-quarterly/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-- jwb@FreeBSD.org --End MAINTAINER-- --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 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/canu/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/canu/work HOME=/wrkdirs/usr/ports/biology/canu/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/canu/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-- DESTDIR=/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/canu/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/canu/work HOME=/wrkdirs/usr/ports/biology/canu/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/canu/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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="gcc6" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing" CPP="cpp6" CPPFLAGS="" LDFLAGS=" -Wl, -rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6" LIBS="" CXX="g++6" CXXFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6" 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-- JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=11.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.24.3 PERL_VER=5.24 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/5.24 DOCSDIR="share/doc/canu" EXAMPLESDIR="share/examples/canu" DATADIR="share/canu" WWWDIR="www/canu" ETCDIR="etc/canu" --End PLIST_SUB-- --SUB_LIST-- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="1.8+" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/canu DOCSDIR=/usr/local/share/doc/canu EXAMPLESDIR=/usr/local/share/examples/canu WWWDIR=/usr/local/www/canu ETCDIR=/usr/local/etc/canu --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 #### ARCH=aarch64 CONFIGURE_MAX_CMD_LEN=262144 OPSYS=FreeBSD OSREL=11.1 OSVERSION=1101001 PYTHONBASE=/usr/local UID=0 _OSRELEASE=11.1-RELEASE #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 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 GPLv2 accepted by the user =========================================================================== =================================================== ===> canu-1.6 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.3_1.txz [111arm64-quarterly-job-20] Installing pkg-1.10.3_1... [111arm64-quarterly-job-20] Extracting pkg-1.10.3_1: .......... done ===> canu-1.6 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of canu-1.6 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by canu-1.6 for building =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by canu-1.6 for building => SHA256 Checksum OK for marbl-canu-v1.6_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by canu-1.6 for building ===> Extracting for canu-1.6 => SHA256 Checksum OK for marbl-canu-v1.6_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for canu-1.6 ===> Applying FreeBSD patches for canu-1.6 /usr/bin/sed -i.bak -e 's|-O4||g' -e 's|-funroll-loops||g' -e 's|-fexpensive-optimizations||g' -e 's|amd64|aarch64|g' /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/Makefile /usr/bin/sed -i.bak -e 's|\\$bin/mhap-|/usr/local/share/java/classes/mhap-|g' /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/pipelines/canu/OverlapMhap.pm /usr/bin/sed -i.bak -e 's|RealBin/lib|RealBin/../lib/perl5/site_perl/canu|g' /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/pipelines/canu.pl =========================================================================== =================================================== ===> canu-1.6 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz [111arm64-quarterly-job-20] Installing gmake-4.2.1_1... [111arm64-quarterly-job-20] `-- Installing gettext-runtime-0.19.8.1_1... [111arm64-quarterly-job-20] | `-- Installing indexinfo-0.3.1... [111arm64-quarterly-job-20] | `-- Extracting indexinfo-0.3.1: .... done [111arm64-quarterly-job-20] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [111arm64-quarterly-job-20] Extracting gmake-4.2.1_1: .......... done ===> canu-1.6 depends on executable: gmake - found ===> Returning to build of canu-1.6 ===> canu-1.6 depends on executable: gcc6 - not found ===> Installing existing package /packages/All/gcc6-6.4.0_3.txz [111arm64-quarterly-job-20] Installing gcc6-6.4.0_3... [111arm64-quarterly-job-20] `-- Installing binutils-2.28,1... [111arm64-quarterly-job-20] `-- Extracting binutils-2.28,1: .......... done [111arm64-quarterly-job-20] `-- Installing gmp-6.1.2... [111arm64-quarterly-job-20] `-- Extracting gmp-6.1.2: .......... done [111arm64-quarterly-job-20] `-- Installing mpc-1.0.3... [111arm64-quarterly-job-20] | `-- Installing mpfr-3.1.6... [111arm64-quarterly-job-20] | `-- Extracting mpfr-3.1.6: .......... done [111arm64-quarterly-job-20] `-- Extracting mpc-1.0.3: ...... done [111arm64-quarterly-job-20] Extracting gcc6-6.4.0_3: .......... done Message from gcc6-6.4.0_3: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc6 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> canu-1.6 depends on executable: gcc6 - found ===> Returning to build of canu-1.6 ===> canu-1.6 depends on file: /usr/local/bin/as - found ===> canu-1.6 depends on package: perl5>=5.24<5.25 - not found ===> Installing existing package /packages/All/perl5-5.24.3.txz [111arm64-quarterly-job-20] Installing perl5-5.24.3... [111arm64-quarterly-job-20] Extracting perl5-5.24.3: .......... done Message from perl5-5.24.3: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> canu-1.6 depends on package: perl5>=5.24<5.25 - found ===> Returning to build of canu-1.6 =========================================================================== =================================================== ===> canu-1.6 depends on shared library: libboost_regex.so - not found ===> Installing existing package /packages/All/boost-libs-1.65.1_1.txz [111arm64-quarterly-job-20] Installing boost-libs-1.65.1_1... [111arm64-quarterly-job-20] `-- Installing icu-60.2_1,1... [111arm64-quarterly-job-20] `-- Extracting icu-60.2_1,1: .......... done [111arm64-quarterly-job-20] Extracting boost-libs-1.65.1_1: .......... done Message from boost-libs-1.65.1_1: You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> canu-1.6 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) ===> Returning to build of canu-1.6 =========================================================================== =================================================== ===> Configuring for canu-1.6 =========================================================================== =================================================== ===> Building for canu-1.6 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src' Building for 'FreeBSD' '1101001' as 'arm64' into '/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm64/{bin,obj}' CC gcc6 6.4.0 CXX g++6 6.4.0 Building release v1.6 g++6 -o /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm64/obj/libcanu.a/AS_global.o -c -MD -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -DNOBACKTRACE -I/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon AS_global.C AS_global.C: In function 'int AS_configure(int, char**)': AS_global.C:101:24: error: 'omp_set_num_threads' was not declared in this scope omp_set_num_threads(1); ^ gmake[1]: *** [Makefile:655: /wrkdirs/usr/ports/biology/canu/work/canu-1.6/src/usr/local/FreeBSD-arm64/obj/libcanu.a/AS_global.o] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/canu/work/canu-1.6/src' *** Error code 1 Stop. make: stopped in /usr/ports/biology/canu