Date: Sat, 13 Nov 2021 14:53:05 GMT From: pkg-fallout@FreeBSD.org To: jwb@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - main-amd64-default][biology/gemma] Failed for gemma-0.98.3_1 in build Message-ID: <202111131453.1ADEr5ID096685@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: jwb@FreeBSD.org Log URL: http://beefy18.nyi.freebsd.org/data/main-amd64-default/p0bef5c19453e_sd032cda0d0/logs/gemma-0.98.3_1.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=main-amd64-default&build=p0bef5c19453e_sd032cda0d0 Log: =>> Building biology/gemma build started at Sat Nov 13 14:52:38 UTC 2021 port directory: /usr/ports/biology/gemma package name: gemma-0.98.3_1 building for: FreeBSD main-amd64-default-job-08 14.0-CURRENT FreeBSD 14.0-CURRENT 1400041 amd64 maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400008 Jail OSVERSION: 1400041 Job Id: 08 !!! Jail is newer than host. (Jail: 1400041, Host: 1400008) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400041 UNAME_v=FreeBSD 14.0-CURRENT 1400041 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=3.2.8-21-g883afb07 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--- ===> The following configuration options are available for gemma-0.98.3_1: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gemma/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gemma/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gemma/work/.cache HOME=/wrkdirs/usr/ports/biology/gemma/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gemma/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/gemma/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gemma/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gemma/work/.cache HOME=/wrkdirs/usr/ports/biology/gemma/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gemma/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 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=" -lopenblas -pthread -L/usr/local/lib -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0 644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTEXAMPLES="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gemma" EXAMPLESDIR="share/examples/gemma" DATADIR="share/gemma" WWWDIR="www/gemma" ETCDIR="etc/gemma" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gemma DOCSDIR=/usr/local/share/doc/gemma EXAMPLESDIR=/usr/local/share/examples/gemma WWWDIR=/usr/local/www/gemma ETCDIR=/usr/local/etc/gemma --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 #### _CCVERSION_921dbbb2=FreeBSD clang version 12.0.1 (git@github.com:llvm/llvm-project.git llvmorg-12.0.1-0-gfed41342a82f) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 12.0.1 (git@github.com:llvm/llvm-project.git llvmorg-12.0.1-0-gfed41342a82f) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--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 12.0.1 (git@github.com:llvm/llvm-project.git llvmorg-12.0.1-0-gfed41342a82f) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400041 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES 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) 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 >============================ ===> gemma-0.98.3_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.17.5.pkg [main-amd64-default-job-08] Installing pkg-1.17.5... [main-amd64-default-job-08] Extracting pkg-1.17.5: .......... done ===> gemma-0.98.3_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gemma-0.98.3_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by gemma-0.98.3_1 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by gemma-0.98.3_1 for building => SHA256 Checksum OK for genetics-statistics-GEMMA-0.98.3_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by gemma-0.98.3_1 for building ===> Extracting for gemma-0.98.3_1 => SHA256 Checksum OK for genetics-statistics-GEMMA-0.98.3_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for gemma-0.98.3_1 ===> Applying FreeBSD patches for gemma-0.98.3_1 from /usr/ports/biology/gemma/files =========================================================================== =======================<phase: build-depends >============================ ===> gemma-0.98.3_1 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found ===> Installing existing package /packages/All/eigen-3.3.9_1.pkg [main-amd64-default-job-08] Installing eigen-3.3.9_1... [main-amd64-default-job-08] `-- Installing blas-3.10.0... [main-amd64-default-job-08] | `-- Installing gcc10-10.3.0... [main-amd64-default-job-08] | | `-- Installing binutils-2.37_2,1... [main-amd64-default-job-08] | | `-- Installing gettext-runtime-0.21... [main-amd64-default-job-08] | | | `-- Installing indexinfo-0.3.1... [main-amd64-default-job-08] | | | `-- Extracting indexinfo-0.3.1: .... done [main-amd64-default-job-08] | | `-- Extracting gettext-runtime-0.21: .......... done [main-amd64-default-job-08] | | `-- Extracting binutils-2.37_2,1: .......... done [main-amd64-default-job-08] | | `-- Installing gmp-6.2.1... [main-amd64-default-job-08] | | `-- Extracting gmp-6.2.1: .......... done [main-amd64-default-job-08] | | `-- Installing mpc-1.2.1... [main-amd64-default-job-08] | | `-- Installing mpfr-4.1.0_1... [main-amd64-default-job-08] | | `-- Extracting mpfr-4.1.0_1: .......... done [main-amd64-default-job-08] | | `-- Extracting mpc-1.2.1: ......... done [main-amd64-default-job-08] | `-- Extracting gcc10-10.3.0: .......... done [main-amd64-default-job-08] `-- Extracting blas-3.10.0: ........ done [main-amd64-default-job-08] `-- Installing lapack-3.10.0_1... [main-amd64-default-job-08] `-- Extracting lapack-3.10.0_1: .......... done [main-amd64-default-job-08] Extracting eigen-3.3.9_1: .......... done ===== Message from gcc10-10.3.0: -- 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. ===> gemma-0.98.3_1 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> Returning to build of gemma-0.98.3_1 ===> gemma-0.98.3_1 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [main-amd64-default-job-08] Installing gmake-4.3_2... [main-amd64-default-job-08] Extracting gmake-4.3_2: .......... done ===> gemma-0.98.3_1 depends on package: gmake>=4.3 - found ===> Returning to build of gemma-0.98.3_1 =========================================================================== =======================<phase: lib-depends >============================ ===> gemma-0.98.3_1 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.7.pkg [main-amd64-default-job-08] Installing gsl-2.7... [main-amd64-default-job-08] Extracting gsl-2.7: .......... done ===> gemma-0.98.3_1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of gemma-0.98.3_1 ===> gemma-0.98.3_1 depends on shared library: libopenblas.so - not found ===> Installing existing package /packages/All/openblas-0.3.18,1.pkg [main-amd64-default-job-08] Installing openblas-0.3.18,1... [main-amd64-default-job-08] Extracting openblas-0.3.18,1: .......... done ===> gemma-0.98.3_1 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> Returning to build of gemma-0.98.3_1 =========================================================================== =======================<phase: configure >============================ ===> Configuring for gemma-0.98.3_1 =========================================================================== =======================<phase: build >============================ ===> Building for gemma-0.98.3_1 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/gemma/work/GEMMA-0.98.3' c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/bslmm.o src/bslmm.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/bslmmdap.o src/bslmmdap.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/debug.o src/debug.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/fastblas.o src/fastblas.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/gemma.o src/gemma.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/gemma_io.o src/gemma_io.cpp src/gemma_io.cpp:892:3: error: reference to 'bitset' is ambiguous bitset<8> b; ^ /usr/include/sys/_bitset.h:64:15: note: candidate found by name lookup is 'bitset' BITSET_DEFINE(bitset, 1); ^ /usr/include/c++/v1/bitset:667:28: note: candidate found by name lookup is 'std::bitset' class _LIBCPP_TEMPLATE_VIS bitset ^ src/gemma_io.cpp:1118:3: error: reference to 'bitset' is ambiguous bitset<8> b; ^ /usr/include/sys/_bitset.h:64:15: note: candidate found by name lookup is 'bitset' BITSET_DEFINE(bitset, 1); ^ /usr/include/c++/v1/bitset:667:28: note: candidate found by name lookup is 'std::bitset' class _LIBCPP_TEMPLATE_VIS bitset ^ src/gemma_io.cpp:1593:3: error: reference to 'bitset' is ambiguous bitset<8> b; ^ /usr/include/sys/_bitset.h:64:15: note: candidate found by name lookup is 'bitset' BITSET_DEFINE(bitset, 1); ^ /usr/include/c++/v1/bitset:667:28: note: candidate found by name lookup is 'std::bitset' class _LIBCPP_TEMPLATE_VIS bitset ^ src/gemma_io.cpp:1950:3: error: reference to 'bitset' is ambiguous bitset<8> b; ^ /usr/include/sys/_bitset.h:64:15: note: candidate found by name lookup is 'bitset' BITSET_DEFINE(bitset, 1); ^ /usr/include/c++/v1/bitset:667:28: note: candidate found by name lookup is 'std::bitset' class _LIBCPP_TEMPLATE_VIS bitset ^ src/gemma_io.cpp:2088:3: error: reference to 'bitset' is ambiguous bitset<8> b; ^ /usr/include/sys/_bitset.h:64:15: note: candidate found by name lookup is 'bitset' BITSET_DEFINE(bitset, 1); ^ /usr/include/c++/v1/bitset:667:28: note: candidate found by name lookup is 'std::bitset' class _LIBCPP_TEMPLATE_VIS bitset ^ src/gemma_io.cpp:2945:3: error: reference to 'bitset' is ambiguous bitset<8> b; ^ /usr/include/sys/_bitset.h:64:15: note: candidate found by name lookup is 'bitset' BITSET_DEFINE(bitset, 1); ^ /usr/include/c++/v1/bitset:667:28: note: candidate found by name lookup is 'std::bitset' class _LIBCPP_TEMPLATE_VIS bitset ^ src/gemma_io.cpp:3674:9: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign] z = z; ~ ^ ~ 1 warning and 6 errors generated. gmake[1]: *** [<builtin>: src/gemma_io.o] Error 1 gmake[1]: *** Waiting for unfinished jobs.... gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/gemma/work/GEMMA-0.98.3' ===> 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/gemma
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