Date: Thu, 27 May 2021 02:49:46 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 130arm64-quarterly][biology/hhsuite] Failed for hhsuite-3.3.0 in build Message-ID: <202105270249.14R2nkuv014710@ampere1.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: yuri@FreeBSD.org Log URL: http://ampere1.nyi.freebsd.org/data/130arm64-quarterly/b3655c33d3de/logs/hhsuite-3.3.0.log Build URL: http://ampere1.nyi.freebsd.org/build.html?mastername=130arm64-quarterly&build=b3655c33d3de Log: =>> Building biology/hhsuite build started at Thu May 27 02:49:11 UTC 2021 port directory: /usr/ports/biology/hhsuite package name: hhsuite-3.3.0 building for: FreeBSD 130arm64-quarterly-job-08 13.0-RELEASE FreeBSD 13.0-RELEASE arm64 maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-8-gaf08dbda Host OSVERSION: 1400008 Jail OSVERSION: 1300139 Job Id: 08 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300139 UNAME_v=FreeBSD 13.0-RELEASE UNAME_r=13.0-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 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=3.2.8-8-gaf08dbda MASTERMNT=/usr/local/poudriere/data/.m/130arm64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/130arm64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=130arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/130arm64-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-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hhsuite/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hhsuite/work HOME=/wrkdirs/usr/ports/biology/hhsuite/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hhsuite/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-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/hhsuite/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/hhsuite/work HOME=/wrkdirs/usr/ports/biology/hhsuite/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/hhsuite/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/biology/hhsuite/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -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" PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_EXT_SUFFIX= PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 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/hhsuite" EXAMPLESDIR="share/examples/hhsuite" DATADIR="share/hhsuite" WWWDIR="www/hhsuite" ETCDIR="etc/hhsuite" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/hhsuite DOCSDIR=/usr/local/share/doc/hhsuite EXAMPLESDIR=/usr/local/share/examples/hhsuite WWWDIR=/usr/local/www/hhsuite ETCDIR=/usr/local/etc/hhsuite --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. 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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 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--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 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=13.0-RELEASE OSREL=13.0 OSVERSION=1300139 PYTHONBASE=/usr/local 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) 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 GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> hhsuite-3.3.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.16.3.txz [130arm64-quarterly-job-08] Installing pkg-1.16.3... [130arm64-quarterly-job-08] Extracting pkg-1.16.3: .......... done ===> hhsuite-3.3.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of hhsuite-3.3.0 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hhsuite-3.3.0 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hhsuite-3.3.0 for building => SHA256 Checksum OK for soedinglab-hh-suite-v3.3.0_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by hhsuite-3.3.0 for building ===> Extracting for hhsuite-3.3.0 => SHA256 Checksum OK for soedinglab-hh-suite-v3.3.0_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for hhsuite-3.3.0 ===> Applying FreeBSD patches for hhsuite-3.3.0 from /usr/ports/biology/hhsuite/files =========================================================================== =======================<phase: build-depends >============================ ===> hhsuite-3.3.0 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.19.6.txz [130arm64-quarterly-job-08] Installing cmake-3.19.6... [130arm64-quarterly-job-08] `-- Installing curl-7.76.0... [130arm64-quarterly-job-08] | `-- Installing ca_root_nss-3.63... [130arm64-quarterly-job-08] | `-- Extracting ca_root_nss-3.63: ........ done [130arm64-quarterly-job-08] | `-- Installing libnghttp2-1.43.0... [130arm64-quarterly-job-08] | `-- Extracting libnghttp2-1.43.0: .......... done [130arm64-quarterly-job-08] `-- Extracting curl-7.76.0: .......... done [130arm64-quarterly-job-08] `-- Installing expat-2.2.10... [130arm64-quarterly-job-08] `-- Extracting expat-2.2.10: .......... done [130arm64-quarterly-job-08] `-- Installing jsoncpp-1.9.4... [130arm64-quarterly-job-08] `-- Extracting jsoncpp-1.9.4: .......... done [130arm64-quarterly-job-08] `-- Installing libarchive-3.5.1,1... [130arm64-quarterly-job-08] | `-- Installing liblz4-1.9.3,1... [130arm64-quarterly-job-08] | `-- Extracting liblz4-1.9.3,1: .......... done [130arm64-quarterly-job-08] `-- Extracting libarchive-3.5.1,1: .......... done [130arm64-quarterly-job-08] `-- Installing libuv-1.41.0... [130arm64-quarterly-job-08] `-- Extracting libuv-1.41.0: .......... done <snip> 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 ===> hhsuite-3.3.0 depends on file: /usr/local/bin/cmake - found ===> Returning to build of hhsuite-3.3.0 ===> hhsuite-3.3.0 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.10.2,2.txz [130arm64-quarterly-job-08] Installing ninja-1.10.2,2... [130arm64-quarterly-job-08] `-- Installing python37-3.7.10... [130arm64-quarterly-job-08] | `-- Installing libffi-3.3_1... [130arm64-quarterly-job-08] | `-- Extracting libffi-3.3_1: .......... done [130arm64-quarterly-job-08] | `-- Installing readline-8.1.0... [130arm64-quarterly-job-08] | `-- Extracting readline-8.1.0: .......... done [130arm64-quarterly-job-08] `-- Extracting python37-3.7.10: .......... done [130arm64-quarterly-job-08] Extracting ninja-1.10.2,2: ........ done ===== Message from python37-3.7.10: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py37-gdbm databases/py-gdbm@py37 py37-sqlite3 databases/py-sqlite3@py37 py37-tkinter x11-toolkits/py-tkinter@py37 ===> hhsuite-3.3.0 depends on executable: ninja - found ===> Returning to build of hhsuite-3.3.0 ===> hhsuite-3.3.0 depends on file: /usr/local/bin/python3.7 - found ===> hhsuite-3.3.0 depends on package: perl5>=5.32.r0<5.33 - not found ===> Installing existing package /packages/All/perl5-5.32.1_1.txz [130arm64-quarterly-job-08] Installing perl5-5.32.1_1... [130arm64-quarterly-job-08] Extracting perl5-5.32.1_1: .......... done ===> hhsuite-3.3.0 depends on package: perl5>=5.32.r0<5.33 - found ===> Returning to build of hhsuite-3.3.0 =========================================================================== =======================<phase: lib-depends >============================ ===> hhsuite-3.3.0 depends on shared library: libmpi.so - not found ===> Installing existing package /packages/All/openmpi-4.1.0_1.txz [130arm64-quarterly-job-08] Installing openmpi-4.1.0_1... [130arm64-quarterly-job-08] `-- Installing gcc10-10.2.0_1... [130arm64-quarterly-job-08] | `-- Installing binutils-2.33.1_4,1... [130arm64-quarterly-job-08] | `-- Extracting binutils-2.33.1_4,1: .......... done [130arm64-quarterly-job-08] | `-- Installing gmp-6.2.1... [130arm64-quarterly-job-08] | `-- Extracting gmp-6.2.1: .......... done [130arm64-quarterly-job-08] | `-- Installing mpc-1.2.0... [130arm64-quarterly-job-08] | | `-- Installing mpfr-4.1.0... [130arm64-quarterly-job-08] | | `-- Extracting mpfr-4.1.0: .......... done [130arm64-quarterly-job-08] | `-- Extracting mpc-1.2.0: ......... done [130arm64-quarterly-job-08] `-- Extracting gcc10-10.2.0_1: .......... done [130arm64-quarterly-job-08] `-- Installing hwloc2-2.4.1... [130arm64-quarterly-job-08] | `-- Installing libpciaccess-0.16... [130arm64-quarterly-job-08] | | `-- Installing pciids-20210223... [130arm64-quarterly-job-08] | | `-- Extracting pciids-20210223: ..... done [130arm64-quarterly-job-08] | `-- Extracting libpciaccess-0.16: ......... done [130arm64-quarterly-job-08] | `-- Installing libxml2-2.9.10_4... [130arm64-quarterly-job-08] | `-- Extracting libxml2-2.9.10_4: .......... done [130arm64-quarterly-job-08] `-- Extracting hwloc2-2.4.1: .......... done [130arm64-quarterly-job-08] `-- Installing libevent-2.1.12... [130arm64-quarterly-job-08] `-- Extracting libevent-2.1.12: .......... done [130arm64-quarterly-job-08] `-- Installing libltdl-2.4.6... [130arm64-quarterly-job-08] `-- Extracting libltdl-2.4.6: .......... done [130arm64-quarterly-job-08] `-- Installing munge-0.5.14_1... [130arm64-quarterly-job-08] `-- Extracting munge-0.5.14_1: ......... done [130arm64-quarterly-job-08] `-- Installing slurm-wlm-20.02.1_6... [130arm64-quarterly-job-08] | `-- Installing hdf-szip-2.1.1... [130arm64-quarterly-job-08] | `-- Extracting hdf-szip-2.1.1: .......... done [130arm64-quarterly-job-08] | `-- Installing hdf5-1.10.6,1... [130arm64-quarterly-job-08] | `-- Extracting hdf5-1.10.6,1: .......... done [130arm64-quarterly-job-08] | `-- Installing json-c-0.15_1... [130arm64-quarterly-job-08] | `-- Extracting json-c-0.15_1: .......... done [130arm64-quarterly-job-08] | `-- Installing libsysinfo-0.0.3_2... [130arm64-quarterly-job-08] | `-- Extracting libsysinfo-0.0.3_2: ......... done [130arm64-quarterly-job-08] | `-- Installing lua52-5.2.4... [130arm64-quarterly-job-08] | | `-- Installing libedit-3.1.20210216,1... [130arm64-quarterly-job-08] | | `-- Extracting libedit-3.1.20210216,1: .......... done [130arm64-quarterly-job-08] | `-- Extracting lua52-5.2.4: ......... done ===> Creating groups. Creating group 'slurm' with gid '468'. ===> Creating users Creating user 'slurm' with uid '468'. [130arm64-quarterly-job-08] `-- Extracting slurm-wlm-20.02.1_6: .......... done [130arm64-quarterly-job-08] Extracting openmpi-4.1.0_1: .......... done ===== Message from gcc10-10.2.0_1: -- 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/gcc10 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> hhsuite-3.3.0 depends on shared library: libmpi.so - found (/usr/local/mpi/openmpi/lib/libmpi.so) ===> Returning to build of hhsuite-3.3.0 =========================================================================== =======================<phase: configure >============================ ===> Configuring for hhsuite-3.3.0 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build -- The C compiler identification is Clang 11.0.1 -- The CXX compiler identification is Clang 11.0.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler is clang(++) -- Looking for fmemopen -- Looking for fmemopen - found -- Found MPI_C: /usr/local/mpi/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/local/mpi/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- xxd not found, using xxdi.pl instead -- Found OpenMP_C: -fopenmp=libomp (found version "5.0") -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_CXX_FOUND) (found version "5.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_COLOR_MAKEFILE CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE Python_ADDITIONAL_VERSIONS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/hhsuite/work/.build =========================================================================== =======================<phase: build >============================ ===> Building for hhsuite-3.3.0 [1/98] /usr/bin/cc -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT 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/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c:172:106: warning: format specifies type 'long long' but the argument has type 'long' [-Wformat] fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); ~~~~ ^~~~~~~~~~~ %ld 1 warning generated. [10/98] /usr/bin/cc -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -I/usr/local/mpi/openmpi/include -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DHAVE_MPI=1 -fexceptions -pthread -MD -MT lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o -MF lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c:172:106: warning: format specifies type 'long long' but the argument has type 'long' [-Wformat] fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status)); ~~~~ ^~~~~~~~~~~ %ld 1 warning generated. 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-I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -I/usr/local/mpi/openmpi/include -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath=-Wl,-rpath=/usr/local/lib/gcc10 -Wl,-rpath -Wl,/usr/local/mpi/openmpi/lib -Wl,--enable-new-dtags -pthread -MD -MT lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o -MF lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o.d -o lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/mpq/mpq.c cc: warning: -Wl,-rpath=-Wl,-rpath=/usr/local/lib/gcc10: 'linker' input unused [-Wunused-command-line-argument] cc: warning: -Wl,-rpath: 'linker' input unused [-Wunused-command-line-argument] cc: warning: -Wl,/usr/local/mpi/openmpi/lib: 'linker' input unused [-Wunused-command-line-argument] cc: warning: -Wl,--enable-new-dtags: 'linker' input unused [-Wunused-command-line-argument] [13/98] : && /usr/local/bin/cmake -E rm -f lib/ffindex/src/mpq/libmpq.a && /usr/bin/ar qc lib/ffindex/src/mpq/libmpq.a lib/ffindex/src/mpq/CMakeFiles/mpq.dir/mpq.c.o && /usr/bin/ranlib lib/ffindex/src/mpq/libmpq.a && : [14/98] /usr/bin/cc -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src/ext -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MD -MT lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -MF lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o.d -o lib/ffindex/src/CMakeFiles/ffindex.dir/ffindex.c.o -c 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lib/ffindex/src/CMakeFiles/ffindex_unpack.dir/ffindex_unpack.c.o -o lib/ffindex/src/ffindex_unpack lib/ffindex/src/libffindex.a && : [18/98] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_modify.dir/ffindex_modify.c.o -o lib/ffindex/src/ffindex_modify lib/ffindex/src/libffindex.a && : [19/98] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_get.dir/ffindex_get.c.o -o lib/ffindex/src/ffindex_get lib/ffindex/src/libffindex.a && : [20/98] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_reduce.dir/ffindex_reduce.c.o -o lib/ffindex/src/ffindex_reduce lib/ffindex/src/libffindex.a && : [21/98] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_from_fasta.dir/ffindex_from_fasta.c.o -o lib/ffindex/src/ffindex_from_fasta lib/ffindex/src/libffindex.a && : [22/98] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_from_fasta_with_split.dir/ffindex_from_fasta_with_split.c.o -o lib/ffindex/src/ffindex_from_fasta_with_split lib/ffindex/src/libffindex.a && : [23/98] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_build.dir/ffindex_build.c.o -o lib/ffindex/src/ffindex_build lib/ffindex/src/libffindex.a && : [24/98] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong -Wl,-rpath=-Wl,-rpath=/usr/local/lib/gcc10 -Wl,-rpath -Wl,/usr/local/mpi/openmpi/lib -Wl,--enable-new-dtags -pthread lib/ffindex/src/CMakeFiles/ffindex_apply_mpi.dir/ffindex_apply_mpi.c.o -o lib/ffindex/src/ffindex_apply_mpi -Wl,-rpath,/usr/local/mpi/openmpi/lib: lib/ffindex/src/libffindex.a lib/ffindex/src/mpq/libmpq.a /usr/local/mpi/openmpi/lib/libmpi.so && : [25/98] : && /usr/bin/cc -std=c99 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/mpi/openmpi/lib -L/usr/local/mpi/openmpi/lib -lmpi -fstack-protector-strong lib/ffindex/src/CMakeFiles/ffindex_apply.dir/ffindex_apply_mpi.c.o -o lib/ffindex/src/ffindex_apply lib/ffindex/src/libffindex.a && : [26/98] cd /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/data && mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated && /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/cmake/xxdi.pl context_data.lib > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h.tmp && mv -f /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h.tmp /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.lib.h [27/98] cd /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/data && mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated && /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/cmake/xxdi.pl context_data.crf > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h.tmp && mv -f /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h.tmp /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/context_data.crf.h [28/98] /usr/bin/c++ -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -Isrc -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -march=native -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhviterbialgorithm.cpp FAILED: src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o /usr/bin/c++ -Igenerated -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/ffindex/src -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simde -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/lib/simd -Isrc -I/wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/cs -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -std=c++0x -fsigned-char -march=native -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -MD -MT src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -MF src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o.d -o src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/src/hhviterbialgorithm.cpp c++: error: the clang compiler does not support '-march=native' [29/98] cd /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/data && mkdir -p /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated && /wrkdirs/usr/ports/biology/hhsuite/work/hh-suite-3.3.0/cmake/xxdi.pl cs219.lib > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h && /usr/bin/sed 's!unsigned char!static const unsigned char!' < /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h > /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h.tmp && mv -f /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h.tmp /wrkdirs/usr/ports/biology/hhsuite/work/.build/generated/cs219.lib.h 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/biology/hhsuite
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