Date: Thu, 12 Aug 2021 04:43:01 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 130releng-riscv64-quarterly][biology/mmseqs2] Failed for MMseqs2-13.45111_2 in configure Message-ID: <202108120443.17C4h1uv038089@beefy7.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: jwb@FreeBSD.org Log URL: http://beefy7.nyi.freebsd.org/data/130releng-riscv64-quarterly/1c54e3e2f7a1/logs/MMseqs2-13.45111_2.log Build URL: http://beefy7.nyi.freebsd.org/build.html?mastername=130releng-riscv64-quarterly&build=1c54e3e2f7a1 Log: =>> Building biology/mmseqs2 build started at Thu Aug 12 04:42:18 UTC 2021 port directory: /usr/ports/biology/mmseqs2 package name: MMseqs2-13.45111_2 building for: FreeBSD 130releng-riscv64-quarterly-job-03 13.0-RELEASE-p3 FreeBSD 13.0-RELEASE-p3 1300139 riscv maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400008 Jail OSVERSION: 1300139 Job Id: 03 ---Begin Environment--- SHELL=/bin/csh UNAME_p=riscv64 UNAME_m=riscv ABI_FILE=/usr/lib/crt1.o OSVERSION=1300139 UNAME_v=FreeBSD 13.0-RELEASE-p3 1300139 UNAME_r=13.0-RELEASE-p3 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 QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-21-g883afb07 MASTERMNT=/usr/local/poudriere/data/.m/130releng-riscv64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/130releng-riscv64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=130releng-riscv64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/130releng-riscv64-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-- 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/mmseqs2/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mmseqs2/work HOME=/wrkdirs/usr/ports/biology/mmseqs2/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mmseqs2/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-- NINJA_STATUS="[%p %s/%t] " PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mmseqs2/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mmseqs2/work HOME=/wrkdirs/usr/ports/biology/mmseqs2/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mmseqs2/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/mmseqs2/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -lpthread -fstack-protector-strong " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -march=rv64imafdc -mabi=lp64d -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 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/MMseqs2" EXAMPLESDIR="share/examples/MMseqs2" DATADIR="share/MMseqs2" WWWDIR="www/MMseqs2" ETCDIR="etc/MMseqs2" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/MMseqs2 DOCSDIR=/usr/local/share/doc/MMseqs2 EXAMPLESDIR=/usr/local/share/examples/MMseqs2 WWWDIR=/usr/local/www/MMseqs2 ETCDIR=/usr/local/etc/MMseqs2 --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=riscv MACHINE_ARCH=riscv64 ARCH=${MACHINE_ARCH} #### /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_9d218390=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: riscv64-unknown-freebsd13.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: riscv64-unknown-freebsd13.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-m" "elf64lriscv" "-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_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: riscv64-unknown-freebsd13.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=riscv64 OPSYS=FreeBSD _OSRELEASE=13.0-RELEASE-p3 OSREL=13.0 OSVERSION=1300139 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.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-- =======================<phase: check-sanity >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> MMseqs2-13.45111_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.16.3.txz [130releng-riscv64-quarterly-job-03] Installing pkg-1.16.3... [130releng-riscv64-quarterly-job-03] Extracting pkg-1.16.3: .......... done ===> MMseqs2-13.45111_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of MMseqs2-13.45111_2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by MMseqs2-13.45111_2 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by MMseqs2-13.45111_2 for building => SHA256 Checksum OK for soedinglab-MMseqs2-13-45111_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by MMseqs2-13.45111_2 for building ===> Extracting for MMseqs2-13.45111_2 => SHA256 Checksum OK for soedinglab-MMseqs2-13-45111_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for MMseqs2-13.45111_2 ===> Applying FreeBSD patches for MMseqs2-13.45111_2 from /usr/ports/biology/mmseqs2/files =========================================================================== =======================<phase: build-depends >============================ ===> MMseqs2-13.45111_2 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.20.4.txz [130releng-riscv64-quarterly-job-03] Installing cmake-3.20.4... [130releng-riscv64-quarterly-job-03] `-- Installing curl-7.77.0... [130releng-riscv64-quarterly-job-03] | `-- Installing ca_root_nss-3.63... [130releng-riscv64-quarterly-job-03] | `-- Extracting ca_root_nss-3.63: ........ done [130releng-riscv64-quarterly-job-03] | `-- Installing libnghttp2-1.43.0... [130releng-riscv64-quarterly-job-03] | `-- Extracting libnghttp2-1.43.0: .......... done [130releng-riscv64-quarterly-job-03] `-- Extracting curl-7.77.0: .......... done [130releng-riscv64-quarterly-job-03] `-- Installing expat-2.4.1... [130releng-riscv64-quarterly-job-03] `-- Extracting expat-2.4.1: .......... done [130releng-riscv64-quarterly-job-03] `-- Installing jsoncpp-1.9.4... [130releng-riscv64-quarterly-job-03] `-- Extracting jsoncpp-1.9.4: .......... done [130releng-riscv64-quarterly-job-03] `-- Installing libarchive-3.5.1,1... [130releng-riscv64-quarterly-job-03] | `-- Installing liblz4-1.9.3,1... [130releng-riscv64-quarterly-job-03] | `-- Extracting liblz4-1.9.3,1: .......... done [130releng-riscv64-quarterly-job-03] `-- Extracting libarchive-3.5.1,1: .......... done [130releng-riscv64-quarterly-job-03] `-- Installing libuv-1.41.0... [130releng-riscv64-quarterly-job-03] `-- Extracting libuv-1.41.0: .......... done [130releng-riscv64-quarterly-job-03] `-- Installing rhash-1.4.1... [130releng-riscv64-quarterly-job-03] | `-- Installing gettext-runtime-0.21... [130releng-riscv64-quarterly-job-03] | | `-- Installing indexinfo-0.3.1... [130releng-riscv64-quarterly-job-03] | | `-- Extracting indexinfo-0.3.1: .... done [130releng-riscv64-quarterly-job-03] | `-- Extracting gettext-runtime-0.21: .......... done [130releng-riscv64-quarterly-job-03] `-- Extracting rhash-1.4.1: .......... done [130releng-riscv64-quarterly-job-03] Extracting cmake-3.20.4: .......... done ===== Message from ca_root_nss-3.63: -- 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. 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 ===> MMseqs2-13.45111_2 depends on file: /usr/local/bin/cmake - found ===> Returning to build of MMseqs2-13.45111_2 ===> MMseqs2-13.45111_2 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.10.2,2.txz [130releng-riscv64-quarterly-job-03] Installing ninja-1.10.2,2... [130releng-riscv64-quarterly-job-03] `-- Installing python38-3.8.10... [130releng-riscv64-quarterly-job-03] | `-- Installing libffi-3.3_1... [130releng-riscv64-quarterly-job-03] | `-- Extracting libffi-3.3_1: .......... done [130releng-riscv64-quarterly-job-03] | `-- Installing mpdecimal-2.5.1... [130releng-riscv64-quarterly-job-03] | `-- Extracting mpdecimal-2.5.1: .......... done [130releng-riscv64-quarterly-job-03] | `-- Installing readline-8.1.1... [130releng-riscv64-quarterly-job-03] | `-- Extracting readline-8.1.1: .......... done [130releng-riscv64-quarterly-job-03] `-- Extracting python38-3.8.10: .......... done [130releng-riscv64-quarterly-job-03] Extracting ninja-1.10.2,2: ........ done ===== Message from python38-3.8.10: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py38-gdbm databases/py-gdbm@py38 py38-sqlite3 databases/py-sqlite3@py38 py38-tkinter x11-toolkits/py-tkinter@py38 ===> MMseqs2-13.45111_2 depends on executable: ninja - found ===> Returning to build of MMseqs2-13.45111_2 ===> MMseqs2-13.45111_2 depends on package: perl5>=5.32.r0<5.33 - not found ===> Installing existing package /packages/All/perl5-5.32.1_1.txz [130releng-riscv64-quarterly-job-03] Installing perl5-5.32.1_1... [130releng-riscv64-quarterly-job-03] Extracting perl5-5.32.1_1: .......... done ===> MMseqs2-13.45111_2 depends on package: perl5>=5.32.r0<5.33 - found ===> Returning to build of MMseqs2-13.45111_2 =========================================================================== =======================<phase: lib-depends >============================ ===> MMseqs2-13.45111_2 depends on shared library: libzstd.so - not found ===> Installing existing package /packages/All/zstd-1.5.0.txz [130releng-riscv64-quarterly-job-03] Installing zstd-1.5.0... [130releng-riscv64-quarterly-job-03] Extracting zstd-1.5.0: .......... done ===> MMseqs2-13.45111_2 depends on shared library: libzstd.so - found (/usr/local/lib/libzstd.so) ===> Returning to build of MMseqs2-13.45111_2 =========================================================================== =======================<phase: configure >============================ ===> Configuring for MMseqs2-13.45111_2 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/mmseqs2/work/.build -- The CXX compiler identification is Clang 11.0.1 -- The C compiler identification is Clang 11.0.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /nxb-bin/usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /nxb-bin/usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Source Directory: /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111 -- Project Directory: /wrkdirs/usr/ports/biology/mmseqs2/work/MMseqs2-13-45111 -- Compiler is clang(++) CMake Warning at CMakeLists.txt:83 (message): CPU without native SIMD instructions. Performance will be bad. -- Found ZSTD: /usr/local/lib/libzstd.a -- xxd not found, using xxdi.pl instead -- ShellCheck disabled -- Performing Test HAVE_POSIX_FADVISE -- Performing Test HAVE_POSIX_FADVISE - Success -- Performing Test HAVE_POSIX_MADVISE -- Performing Test HAVE_POSIX_MADVISE - Success -- OMPTL sorting fallback -- Found ZLIB -- Performing Test HAVE_ZLIB_CHECK -- Performing Test HAVE_ZLIB_CHECK - Success -- ZLIB works -- Found BZLIB -- Performing Test HAVE_BZLIB_CHECK -- Performing Test HAVE_BZLIB_CHECK - Success -- BZLIB works CMake Error at src/CMakeLists.txt:228 (message): -- Could not find OpenMP. Skip check with -DREQUIRE_OPENMP=0. -- Configuring incomplete, errors occurred! See also "/wrkdirs/usr/ports/biology/mmseqs2/work/.build/CMakeFiles/CMakeOutput.log". See also "/wrkdirs/usr/ports/biology/mmseqs2/work/.build/CMakeFiles/CMakeError.log". *** Error code 1 Stop. make: stopped in /usr/ports/biology/mmseqs2
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