Date: Thu, 26 Oct 2017 10:27:15 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110arm64-default][biology/iqtree] Failed for iqtree-1.6.b4_1 in build Message-ID: <201710261027.v9QARFiW018065@thunderx1.nyi.freebsd.org>
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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: jrm@FreeBSD.org Last committer: jrm@FreeBSD.org Ident: $FreeBSD: head/biology/iqtree/Makefile 452596 2017-10-21 17:40:18Z jrm $ Log URL: http://thunderx1.nyi.freebsd.org/data/110arm64-default/452754/logs/iqtree-1.6.b4_1.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=110arm64-default&build=452754 Log: ====>> Building biology/iqtree build started at Thu Oct 26 10:26:07 UTC 2017 port directory: /usr/ports/biology/iqtree building for: FreeBSD 110arm64-default-job-10 11.0-RELEASE-p1 FreeBSD 11.0-RELEASE-p1 arm64 maintained by: jrm@FreeBSD.org Makefile ident: $FreeBSD: head/biology/iqtree/Makefile 452596 2017-10-21 17:40:18Z jrm $ Poudriere version: 3.1.21-7-g66ad3813 Host OSVERSION: 1200044 Jail OSVERSION: 1100122 Job Id: 10 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1100122 UNAME_v=FreeBSD 11.0-RELEASE-p1 UNAME_r=11.0-RELEASE-p1 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110arm64-default/ref PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=iqtree-1.6.b4_1 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/110arm64-default/ref/.p/pool MASTERNAME=110arm64-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.21-7-g66ad3813 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for iqtree-1.6.b4_1: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/iqtree/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/iqtree/work HOME=/wrkdirs/usr/ports/biology/iqtree/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/iqtree/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/biology/iqtree/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/iqtree/work HOME=/wrkdirs/usr/ports/biology/iqtree/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/iqtree/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" DESTDIR=/wrkdirs/usr/ports/biology/iqtree/work/stage 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/l ib/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-- CMAKE_BUILD_TYPE="release" OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/iqtree" EXAMPLESDIR="share/examples/iqtree" DATADIR="share/iqtree" WWWDIR="www/iqtree" ETCDIR="etc/iqtree" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/iqtree DOCSDIR=/usr/local/share/doc/iqtree EXAMPLESDIR=/usr/local/share/examples/iqtree WWWDIR=/usr/local/www/iqtree ETCDIR=/usr/local/etc/iqtree --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=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=11.0 OSVERSION=1100122 PYTHONBASE=/usr/local UID=0 _JAVA_OS_LIST_REGEXP=native|linux _JAVA_VENDOR_LIST_REGEXP=openjdk|oracle|sun _JAVA_VERSION_LIST_REGEXP=1.6|1.7|1.8|1.9|1.6\+|1.7\+|1.8\+|1.9\+ _OSRELEASE=11.0-RELEASE-p1 #### Misc Poudriere #### GID=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-- =======================<phase: check-sanity >============================ ===> License GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> iqtree-1.6.b4_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz [110arm64-default-job-10] Installing pkg-1.10.1... [110arm64-default-job-10] Extracting pkg-1.10.1: .......... done ===> iqtree-1.6.b4_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of iqtree-1.6.b4_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user => Cibiv-iqtree-v1.6.beta4_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/Cibiv/iqtree/tar.gz/v1.6.beta4?dummy=/Cibiv-iqtree-v1.6.beta4_GH0.tar.gz fetch: https://codeload.github.com/Cibiv/iqtree/tar.gz/v1.6.beta4?dummy=/Cibiv-iqtree-v1.6.beta4_GH0.tar.gz: size unknown fetch: https://codeload.github.com/Cibiv/iqtree/tar.gz/v1.6.beta4?dummy=/Cibiv-iqtree-v1.6.beta4_GH0.tar.gz: size of remote file is not known Cibiv-iqtree-v1.6.beta4_GH0.tar.gz 0 B 0 Bps ===> Fetching all distfiles required by iqtree-1.6.b4_1 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by iqtree-1.6.b4_1 for building => SHA256 Checksum OK for Cibiv-iqtree-v1.6.beta4_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by iqtree-1.6.b4_1 for building ===> Extracting for iqtree-1.6.b4_1 => SHA256 Checksum OK for Cibiv-iqtree-v1.6.beta4_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for iqtree-1.6.b4_1 =========================================================================== =======================<phase: build-depends >============================ ===> iqtree-1.6.b4_1 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found ===> Installing existing package /packages/All/eigen-3.3.4.txz [110arm64-default-job-10] Installing eigen-3.3.4... [110arm64-default-job-10] Extracting eigen-3.3.4: .......... done ===> iqtree-1.6.b4_1 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> Returning to build of iqtree-1.6.b4_1 ===> iqtree-1.6.b4_1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.9.4.txz [110arm64-default-job-10] Installing cmake-3.9.4... [110arm64-default-job-10] `-- Installing curl-7.56.0... [110arm64-default-job-10] | `-- Installing ca_root_nss-3.32.1... [110arm64-default-job-10] | `-- Extracting ca_root_nss-3.32.1: ........ done [110arm64-default-job-10] | `-- Installing libnghttp2-1.26.0... [110arm64-default-job-10] | `-- Extracting libnghttp2-1.26.0: .......... done [110arm64-default-job-10] `-- Extracting curl-7.56.0: .......... done [110arm64-default-job-10] `-- Installing expat-2.2.1... [110arm64-default-job-10] `-- Extracting expat-2.2.1: .......... done [110arm64-default-job-10] `-- Installing jsoncpp-1.8.1_2... [110arm64-default-job-10] `-- Extracting jsoncpp-1.8.1_2: .......... done [110arm64-default-job-10] `-- Installing libarchive-3.3.1,1... [110arm64-default-job-10] | `-- Installing liblz4-1.8.0,1... [110arm64-default-job-10] | `-- Extracting liblz4-1.8.0,1: .......... done [110arm64-default-job-10] | `-- Installing lzo2-2.10_1... [110arm64-default-job-10] | `-- Extracting lzo2-2.10_1: .......... done [110arm64-default-job-10] `-- Extracting libarchive-3.3.1,1: .......... done [110arm64-default-job-10] `-- Installing libuv-1.15.0... [110arm64-default-job-10] `-- Extracting libuv-1.15.0: .......... done [110arm64-default-job-10] `-- Installing rhash-1.3.4... [110arm64-default-job-10] `-- Extracting rhash-1.3.4: .......... done [110arm64-default-job-10] Extracting cmake-3.9.4: .......... done Message from ca_root_nss-3.32.1: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> iqtree-1.6.b4_1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of iqtree-1.6.b4_1 ===> iqtree-1.6.b4_1 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.8.2,2.txz [110arm64-default-job-10] Installing ninja-1.8.2,2... [110arm64-default-job-10] `-- Installing python27-2.7.14_1... [110arm64-default-job-10] | `-- Installing gettext-runtime-0.19.8.1_1... [110arm64-default-job-10] | | `-- Installing indexinfo-0.2.6... [110arm64-default-job-10] | | `-- Extracting indexinfo-0.2.6: .... done [110arm64-default-job-10] | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [110arm64-default-job-10] | `-- Installing libffi-3.2.1_1... [110arm64-default-job-10] | `-- Extracting libffi-3.2.1_1: .......... done [110arm64-default-job-10] | `-- Installing readline-7.0.3... [110arm64-default-job-10] | `-- Extracting readline-7.0.3: .......... done [110arm64-default-job-10] `-- Extracting python27-2.7.14_1: .......... done [110arm64-default-job-10] Extracting ninja-1.8.2,2: ....... done Message from python27-2.7.14_1: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> iqtree-1.6.b4_1 depends on executable: ninja - found ===> Returning to build of iqtree-1.6.b4_1 ===> iqtree-1.6.b4_1 depends on executable: gcc6 - not found ===> Installing existing package /packages/All/gcc6-6.4.0_2.txz [110arm64-default-job-10] Installing gcc6-6.4.0_2... [110arm64-default-job-10] `-- Installing binutils-2.28,1... [110arm64-default-job-10] `-- Extracting binutils-2.28,1: .......... done [110arm64-default-job-10] `-- Installing gmp-6.1.2... [110arm64-default-job-10] `-- Extracting gmp-6.1.2: .......... done [110arm64-default-job-10] `-- Installing mpc-1.0.3... [110arm64-default-job-10] | `-- Installing mpfr-3.1.6... [110arm64-default-job-10] | `-- Extracting mpfr-3.1.6: .......... done [110arm64-default-job-10] `-- Extracting mpc-1.0.3: ...... done [110arm64-default-job-10] Extracting gcc6-6.4.0_2: .......... done Message from gcc6-6.4.0_2: 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. ===> iqtree-1.6.b4_1 depends on executable: gcc6 - found ===> Returning to build of iqtree-1.6.b4_1 ===> iqtree-1.6.b4_1 depends on file: /usr/local/bin/as - found =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for iqtree-1.6.b4_1 ===> Performing in-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-1.6.beta4 -- The C compiler identification is GNU 6.4.0 -- The CXX compiler identification is GNU 6.4.0 -- Check for working C compiler: /usr/local/bin/gcc6 -- Check for working C compiler: /usr/local/bin/gcc6 -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/local/bin/g++6 -- Check for working CXX compiler: /usr/local/bin/g++6 -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done IQ-TREE flags : Builde mode : Release Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 C flags : -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections CXX flags : -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections LINKER flags : -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for backtrace -- Looking for backtrace - not found -- Found Backtrace: /usr/lib/libexecinfo.so -- Found ZLIB: /usr/lib/libz.so (found version "1.2.8") Using system zlib -- Found Eigen3: /usr/local/include/eigen3 (Required is at least version "2.91.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/iqtree/work/IQ-TREE-1.6.beta4 =========================================================================== =======================<phase: build >============================ ===> Building for iqtree-1.6.b4_1 [1/172] /usr/local/bin/g++6 -DIQ_TREE -D_USE_PTHREADS -I. -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c vectorclass/instrset_detect.cpp FAILED: vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/local/bin/g++6 -DIQ_TREE -D_USE_PTHREADS -I. -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc6 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc6 -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c vectorclass/instrset_detect.cpp g++6: error: unrecognized command line option '-msse3'; did you mean '-assert'? ninja: build stopped: subcommand failed. *** Error code 1 Stop. make: stopped in /usr/ports/biology/iqtree
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