Date: Tue, 16 Feb 2021 15:25:26 GMT From: pkg-fallout@FreeBSD.org To: yuri@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - main-amd64-default][biology/spoa] Failed for spoa-4.0.7 in build Message-ID: <202102161525.11GFPQw9021890@beefy18.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 Last committer: yuri@FreeBSD.org Ident: $FreeBSD: head/biology/spoa/Makefile 562036 2021-01-19 09:28:00Z yuri $ Log URL: http://beefy18.nyi.freebsd.org/data/main-amd64-default/p565379_s10fc4c3218/logs/spoa-4.0.7.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=main-amd64-default&build=p565379_s10fc4c3218 Log: =>> Building biology/spoa build started at Tue Feb 16 15:24:55 UTC 2021 port directory: /usr/ports/biology/spoa package name: spoa-4.0.7 building for: FreeBSD main-amd64-default-job-05 14.0-CURRENT FreeBSD 14.0-CURRENT 1400004 amd64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/biology/spoa/Makefile 562036 2021-01-19 09:28:00Z yuri $ Poudriere version: 3.2.8-8-gaf08dbda Host OSVERSION: 1300134 Jail OSVERSION: 1400004 Job Id: 05 !!! Jail is newer than host. (Jail: 1400004, Host: 1300134) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1400004 UNAME_v=FreeBSD 14.0-CURRENT 1400004 UNAME_r=14.0-CURRENT 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/main-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-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/biology/spoa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/spoa/work HOME=/wrkdirs/usr/ports/biology/spoa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/spoa/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/spoa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/spoa/work HOME=/wrkdirs/usr/ports/biology/spoa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/spoa/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/spoa/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lz -lcpu_features -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/spoa" EXAMPLESDIR="share/examples/spoa" DATADIR="share/spoa" WWWDIR="www/spoa" ETCDIR="etc/spoa" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/spoa DOCSDIR=/usr/local/share/doc/spoa EXAMPLESDIR=/usr/local/share/examples/spoa WWWDIR=/usr/local/www/spoa ETCDIR=/usr/local/etc/spoa --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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[main-amd64-default-job-05] Extracting pkg-1.16.2: .......... done ===> spoa-4.0.7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of spoa-4.0.7 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by spoa-4.0.7 for building =========================================================================== =======================<phase: checksum >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by spoa-4.0.7 for building => SHA256 Checksum OK for rvaser-spoa-4.0.7_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by spoa-4.0.7 for building ===> Extracting for spoa-4.0.7 => SHA256 Checksum OK for rvaser-spoa-4.0.7_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for spoa-4.0.7 ===> Applying FreeBSD patches for spoa-4.0.7 from /usr/ports/biology/spoa/files =========================================================================== =======================<phase: build-depends >============================ ===> spoa-4.0.7 depends on package: bioparser>0 - not found ===> Installing existing package /packages/All/bioparser-3.0.12.2.txz [main-amd64-default-job-05] Installing bioparser-3.0.12.2... [main-amd64-default-job-05] Extracting bioparser-3.0.12.2: .......... done ===> spoa-4.0.7 depends on package: bioparser>0 - found ===> Returning to build of spoa-4.0.7 ===> spoa-4.0.7 depends on file: /usr/local/include/biosoup/nucleic_acid.hpp - not found ===> Installing existing package /packages/All/biosoup-g20201216.txz [main-amd64-default-job-05] Installing biosoup-g20201216... [main-amd64-default-job-05] Extracting biosoup-g20201216: ........ done ===> spoa-4.0.7 depends on file: /usr/local/include/biosoup/nucleic_acid.hpp - found ===> Returning to build of spoa-4.0.7 ===> spoa-4.0.7 depends on package: cereal>0 - not found ===> Installing existing package /packages/All/cereal-1.3.0.10.txz [main-amd64-default-job-05] Installing cereal-1.3.0.10... [main-amd64-default-job-05] `-- Installing boost-libs-1.72.0_3... [main-amd64-default-job-05] | `-- Installing icu-68.2,1... [main-amd64-default-job-05] | `-- Extracting icu-68.2,1: .......... done [main-amd64-default-job-05] `-- Extracting boost-libs-1.72.0_3: .......... done [main-amd64-default-job-05] Extracting cereal-1.3.0.10: .......... done ===== Message from boost-libs-1.72.0_3: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> spoa-4.0.7 depends on package: cereal>0 - found ===> Returning to build of spoa-4.0.7 ===> spoa-4.0.7 depends on package: cpu_features>0 - not found ===> Installing existing package /packages/All/cpu_features-0.5.0.txz [main-amd64-default-job-05] Installing cpu_features-0.5.0... [main-amd64-default-job-05] Extracting cpu_features-0.5.0: .......... done ===> spoa-4.0.7 depends on package: cpu_features>0 - found ===> Returning to build of spoa-4.0.7 ===> spoa-4.0.7 depends on package: simde>0 - not found ===> Installing existing package /packages/All/simde-0.7.2.txz [main-amd64-default-job-05] Installing simde-0.7.2... [main-amd64-default-job-05] Extracting simde-0.7.2: .......... done ===> spoa-4.0.7 depends on package: simde>0 - found ===> Returning to build of spoa-4.0.7 ===> spoa-4.0.7 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.19.4_1.txz [main-amd64-default-job-05] Installing cmake-3.19.4_1... [main-amd64-default-job-05] `-- Installing curl-7.75.0... [main-amd64-default-job-05] | `-- Installing ca_root_nss-3.61... [main-amd64-default-job-05] | `-- Extracting ca_root_nss-3.61: ........ done [main-amd64-default-job-05] | `-- Installing libnghttp2-1.43.0... [main-amd64-default-job-05] | `-- Extracting libnghttp2-1.43.0: .......... done [main-amd64-default-job-05] `-- Extracting curl-7.75.0: .......... done [main-amd64-default-job-05] `-- Installing expat-2.2.10... [main-amd64-default-job-05] `-- Extracting expat-2.2.10: .......... done [main-amd64-default-job-05] `-- Installing jsoncpp-1.9.4... [main-amd64-default-job-05] `-- Extracting jsoncpp-1.9.4: .......... done [main-amd64-default-job-05] `-- Installing libarchive-3.4.3_1,1... [main-amd64-default-job-05] | `-- Installing liblz4-1.9.3,1... [main-amd64-default-job-05] | `-- Extracting liblz4-1.9.3,1: .......... done [main-amd64-default-job-05] `-- Extracting libarchive-3.4.3_1,1: .......... done [main-amd64-default-job-05] `-- Installing libuv-1.40.0... [main-amd64-default-job-05] `-- Extracting libuv-1.40.0: .......... done [main-amd64-default-job-05] `-- Installing rhash-1.4.1... [main-amd64-default-job-05] | `-- Installing gettext-runtime-0.21... [main-amd64-default-job-05] | | `-- Installing indexinfo-0.3.1... [main-amd64-default-job-05] | | `-- Extracting indexinfo-0.3.1: .... done [main-amd64-default-job-05] | `-- Extracting gettext-runtime-0.21: .......... done [main-amd64-default-job-05] `-- Extracting rhash-1.4.1: .......... done [main-amd64-default-job-05] Extracting cmake-3.19.4_1: .......... done ===== Message from ca_root_nss-3.61: -- 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 ===> spoa-4.0.7 depends on file: /usr/local/bin/cmake - found ===> Returning to build of spoa-4.0.7 ===> spoa-4.0.7 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.10.2,2.txz [main-amd64-default-job-05] Installing ninja-1.10.2,2... [main-amd64-default-job-05] `-- Installing python37-3.7.9_1... [main-amd64-default-job-05] | `-- Installing libffi-3.3_1... [main-amd64-default-job-05] | `-- Extracting libffi-3.3_1: .......... done [main-amd64-default-job-05] | `-- Installing readline-8.1.0... [main-amd64-default-job-05] | `-- Extracting readline-8.1.0: .......... done [main-amd64-default-job-05] `-- Extracting python37-3.7.9_1: .......... done [main-amd64-default-job-05] Extracting ninja-1.10.2,2: ........ done ===== Message from python37-3.7.9_1: -- 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 ===> spoa-4.0.7 depends on executable: ninja - found ===> Returning to build of spoa-4.0.7 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for spoa-4.0.7 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/spoa/work/.build -- The CXX compiler identification is Clang 11.0.1 -- 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 -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE THREADS_HAVE_PTHREAD_ARG spoa_optimize_for_native spoa_optimize_for_portability -- Build files have been written to: /wrkdirs/usr/ports/biology/spoa/work/.build =========================================================================== =======================<phase: build >============================ ===> Building for spoa-4.0.7 [1/11] /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -Dspoa_EXPORTS -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -std=c++11 -MD -MT 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-pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -msse2 -std=c++11 -MD -MT CMakeFiles/spoa_sse2.dir/src/simd_alignment_engine_dispatch.cpp.o -MF CMakeFiles/spoa_sse2.dir/src/simd_alignment_engine_dispatch.cpp.o.d -o CMakeFiles/spoa_sse2.dir/src/simd_alignment_engine_dispatch.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine_dispatch.cpp [5/11] /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -Dspoa_EXPORTS -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -std=c++11 -MD -MT CMakeFiles/spoa.dir/src/dispatcher.cpp.o -MF CMakeFiles/spoa.dir/src/dispatcher.cpp.o.d -o CMakeFiles/spoa.dir/src/dispatcher.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/dispatcher.cpp [6/11] /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/include -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/vendor/simde -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -msse4.1 -std=c++11 -MD -MT CMakeFiles/spoa_sse4.1.dir/src/simd_alignment_engine_dispatch.cpp.o -MF CMakeFiles/spoa_sse4.1.dir/src/simd_alignment_engine_dispatch.cpp.o.d -o CMakeFiles/spoa_sse4.1.dir/src/simd_alignment_engine_dispatch.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine_dispatch.cpp [7/11] /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DSPOA_VERSION=\"v4.0.7\" -DUSE_SIMDE -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -std=c++11 -MD -MT CMakeFiles/spoa_exe.dir/src/main.cpp.o -MF CMakeFiles/spoa_exe.dir/src/main.cpp.o.d -o CMakeFiles/spoa_exe.dir/src/main.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/main.cpp [8/11] /usr/bin/c++ -DGENERATE_DISPATCH -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_ENABLE_OPENMP -DSIMDE_NO_NATIVE -DUSE_SIMDE -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/include -I/wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/vendor/simde -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -mavx2 -std=c++11 -MD -MT CMakeFiles/spoa_avx2.dir/src/simd_alignment_engine_dispatch.cpp.o -MF CMakeFiles/spoa_avx2.dir/src/simd_alignment_engine_dispatch.cpp.o.d -o CMakeFiles/spoa_avx2.dir/src/simd_alignment_engine_dispatch.cpp.o -c /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/simd_alignment_engine_dispatch.cpp [9/11] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -lz -lcpu_features -fstack-protector-strong -L/usr/local/lib -shared -Wl,-soname,libspoa.so.7.0.0 -o lib/libspoa.so.7.0.0 CMakeFiles/spoa.dir/src/alignment_engine.cpp.o CMakeFiles/spoa.dir/src/graph.cpp.o CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o CMakeFiles/spoa.dir/src/dispatcher.cpp.o -lcereal && : FAILED: lib/libspoa.so.7.0.0 : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wall -Wextra -pedantic -fopenmp-simd -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -lz -lcpu_features -fstack-protector-strong -L/usr/local/lib -shared -Wl,-soname,libspoa.so.7.0.0 -o lib/libspoa.so.7.0.0 CMakeFiles/spoa.dir/src/alignment_engine.cpp.o CMakeFiles/spoa.dir/src/graph.cpp.o CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o CMakeFiles/spoa.dir/src/dispatcher.cpp.o -lcereal && : ld: error: unable to find library -lcereal c++: error: linker command failed with exit code 1 (use -v to see invocation) 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/spoa
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