[package - main-amd64-default][science/helfem] Failed for helfem-g20210912_1 in configure
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Date: Thu, 30 Dec 2021 01:41:59 UTC
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://beefy18.nyi.freebsd.org/data/main-amd64-default/pb62f24f32e66_sc3a688ef4d/logs/helfem-g20210912_1.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=main-amd64-default&build=pb62f24f32e66_sc3a688ef4d Log: =>> Building science/helfem build started at Thu Dec 30 01:41:36 UTC 2021 port directory: /usr/ports/science/helfem package name: helfem-g20210912_1 building for: FreeBSD main-amd64-default-job-10 14.0-CURRENT FreeBSD 14.0-CURRENT 1400045 amd64 maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400042 Jail OSVERSION: 1400045 Job Id: 10 !!! Jail is newer than host. (Jail: 1400045, Host: 1400042) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400045 UNAME_v=FreeBSD 14.0-CURRENT 1400045 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--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran10" FC="gfortran10" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc10" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc10" XDG_DATA_HOME=/wrkdirs/usr/ports/science/helfem/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/helfem/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/helfem/work/.cache HOME=/wrkdirs/usr/ports/science/helfem/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/helfem/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-- F77="gfortran10" FC="gfortran10" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc10" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc10" XDG_DATA_HOME=/wrkdirs/usr/ports/science/helfem/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/helfem/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/helfem/work/.cache HOME=/wrkdirs/usr/ports/science/helfem/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/helfem/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" PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fst ack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc10 -L/usr/local/lib/gcc10 -B/usr/local/bin -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" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/helfem" EXAMPLESDIR="share/examples/helfem" DATADIR="share/helfem" WWWDIR="www/helfem" ETCDIR="etc/helfem" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/helfem DOCSDIR=/usr/local/share/doc/helfem EXAMPLESDIR=/usr/local/share/examples/helfem WWWDIR=/usr/local/www/helfem ETCDIR=/usr/local/etc/helfem --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 #### _CXXINTERNAL_acaad9ca=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "c++" CC_OUTPUT_921dbbb2_58173849=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" CC_OUTPUT_921dbbb2_9bdba57c=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" CC_OUTPUT_921dbbb2_6a4fe7f5=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" CC_OUTPUT_921dbbb2_6bcac02b=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" CC_OUTPUT_921dbbb2_67d20829=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" CC_OUTPUT_921dbbb2_bfa62e83=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" CC_OUTPUT_921dbbb2_f0b4d593=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" CC_OUTPUT_921dbbb2_308abb44=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" CC_OUTPUT_921dbbb2_f00456e5=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" CC_OUTPUT_921dbbb2_65ad290d=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" CC_OUTPUT_921dbbb2_f2776b26=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" CC_OUTPUT_921dbbb2_b2657cc3=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" CC_OUTPUT_921dbbb2_380987f7=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" CC_OUTPUT_921dbbb2_160933ec=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" CC_OUTPUT_921dbbb2_fb62803b=ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400045 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 GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> helfem-g20210912_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.17.5.pkg [main-amd64-default-job-10] Installing pkg-1.17.5... [main-amd64-default-job-10] Extracting pkg-1.17.5: .......... done ===> helfem-g20210912_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of helfem-g20210912_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by helfem-g20210912_1 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by helfem-g20210912_1 for building => SHA256 Checksum OK for susilehtola-HelFEM-g20210912-21461e9_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by helfem-g20210912_1 for building ===> Extracting for helfem-g20210912_1 => SHA256 Checksum OK for susilehtola-HelFEM-g20210912-21461e9_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for helfem-g20210912_1 =========================================================================== =======================<phase: build-depends >============================ ===> helfem-g20210912_1 depends on file: /usr/local/bin/cmake - not found ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" make[1]: "/usr/ports/Mk/Uses/compiler.mk" line 73: warning: "cc --version" returned non-zero status ld-elf.so.1: Shared object "libc++.so.1" not found, required by "clang" make[1]: "/usr/ports/Mk/Uses/compiler.mk" line 92: warning: "/usr/bin/clang --version" returned non-zero status ===> Installing existing package /packages/All/cmake-3.22.1.pkg [main-amd64-default-job-10] Installing cmake-3.22.1... [main-amd64-default-job-10] `-- Installing curl-7.80.0... [main-amd64-default-job-10] | `-- Installing ca_root_nss-3.71... [main-amd64-default-job-10] | `-- Extracting ca_root_nss-3.71: ........ done [main-amd64-default-job-10] | `-- Installing libnghttp2-1.46.0... [main-amd64-default-job-10] | `-- Extracting libnghttp2-1.46.0: .......... done [main-amd64-default-job-10] | `-- Installing libssh2-1.10.0,3... <snip> Message from ca_root_nss-3.71: -- 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 ===> helfem-g20210912_1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of helfem-g20210912_1 ===> helfem-g20210912_1 depends on executable: gfortran10 - not found ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" make[1]: "/usr/ports/Mk/Uses/compiler.mk" line 73: warning: "cc --version" returned non-zero status ld-elf.so.1: Shared object "libc++.so.1" not found, required by "clang" make[1]: "/usr/ports/Mk/Uses/compiler.mk" line 92: warning: "/usr/bin/clang --version" returned non-zero status ===> Installing existing package /packages/All/gcc10-10.3.0.pkg [main-amd64-default-job-10] Installing gcc10-10.3.0... [main-amd64-default-job-10] `-- Installing binutils-2.37_2,1... [main-amd64-default-job-10] `-- Extracting binutils-2.37_2,1: .......... done [main-amd64-default-job-10] `-- Installing gmp-6.2.1... [main-amd64-default-job-10] `-- Extracting gmp-6.2.1: .......... done [main-amd64-default-job-10] `-- Installing mpc-1.2.1... [main-amd64-default-job-10] | `-- Installing mpfr-4.1.0_1... [main-amd64-default-job-10] | `-- Extracting mpfr-4.1.0_1: .......... done [main-amd64-default-job-10] `-- Extracting mpc-1.2.1: ......... done [main-amd64-default-job-10] Extracting gcc10-10.3.0: .......... 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. ===> helfem-g20210912_1 depends on executable: gfortran10 - found ===> Returning to build of helfem-g20210912_1 ===> helfem-g20210912_1 depends on file: /usr/local/bin/as - found =========================================================================== =======================<phase: lib-depends >============================ ===> helfem-g20210912_1 depends on shared library: libarmadillo.so - not found ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cc" make[1]: "/usr/ports/Mk/Uses/compiler.mk" line 73: warning: "cc --version" returned non-zero status ld-elf.so.1: Shared object "libc++.so.1" not found, required by "clang" make[1]: "/usr/ports/Mk/Uses/compiler.mk" line 92: warning: "/usr/bin/clang --version" returned non-zero status ===> Installing existing package /packages/All/armadillo-10.7.1.pkg [main-amd64-default-job-10] Installing armadillo-10.7.1... [main-amd64-default-job-10] `-- Installing arpack-ng-3.8.0... [main-amd64-default-job-10] | `-- Installing blas-3.10.0... [main-amd64-default-job-10] | `-- Extracting blas-3.10.0: ........ done [main-amd64-default-job-10] | `-- Installing lapack-3.10.0_1... [main-amd64-default-job-10] | `-- Extracting lapack-3.10.0_1: .......... done [main-amd64-default-job-10] | `-- Installing mpich-3.4.3... [main-amd64-default-job-10] | | `-- Installing bash-5.1.12... [main-amd64-default-job-10] | | `-- Installing readline-8.1.1... [main-amd64-default-job-10] | | `-- Extracting readline-8.1.1: .......... done [main-amd64-default-job-10] | | `-- Extracting bash-5.1.12: .......... done [main-amd64-default-job-10] | | `-- Installing hwloc2-2.5.0... [main-amd64-default-job-10] | | `-- Installing level-zero-1.7.4... [main-amd64-default-job-10] | | `-- Extracting level-zero-1.7.4: .......... done [main-amd64-default-job-10] | | `-- Installing libpciaccess-0.16... [main-amd64-default-job-10] | | | `-- Installing pciids-20211124... [main-amd64-default-job-10] | | | `-- Extracting pciids-20211124: ..... done [main-amd64-default-job-10] | | `-- Extracting libpciaccess-0.16: ......... done [main-amd64-default-job-10] | | `-- Installing libxml2-2.9.12... [main-amd64-default-job-10] | | `-- Extracting libxml2-2.9.12: .......... done [main-amd64-default-job-10] | | `-- Extracting hwloc2-2.5.0: .......... done [main-amd64-default-job-10] | | `-- Installing json-c-0.15_1... [main-amd64-default-job-10] | | `-- Extracting json-c-0.15_1: .......... done [main-amd64-default-job-10] | | `-- Installing libepoll-shim-0.0.20210418... [main-amd64-default-job-10] | | `-- Extracting libepoll-shim-0.0.20210418: .......... done [main-amd64-default-job-10] | | `-- Installing libfabric-1.14.0... [main-amd64-default-job-10] | | `-- Extracting libfabric-1.14.0: .......... done [main-amd64-default-job-10] | | `-- Installing perl5-5.32.1_1... [main-amd64-default-job-10] | | `-- Extracting perl5-5.32.1_1: .......... done [main-amd64-default-job-10] | | `-- Installing slurm-wlm-20.02.7... [main-amd64-default-job-10] | | `-- Installing hdf-szip-2.1.1... [main-amd64-default-job-10] | | `-- Extracting hdf-szip-2.1.1: .......... done [main-amd64-default-job-10] | | `-- Installing hdf5-1.10.6,1... [main-amd64-default-job-10] | | `-- Extracting hdf5-1.10.6,1: .......... done [main-amd64-default-job-10] | | `-- Installing libsysinfo-0.0.3_2... [main-amd64-default-job-10] | | `-- Extracting libsysinfo-0.0.3_2: ......... done [main-amd64-default-job-10] | | `-- Installing lua52-5.2.4... [main-amd64-default-job-10] | | | `-- Installing libedit-3.1.20210216,1... [main-amd64-default-job-10] | | | `-- Extracting libedit-3.1.20210216,1: .......... done [main-amd64-default-job-10] | | `-- Extracting lua52-5.2.4: ......... done [main-amd64-default-job-10] | | `-- Installing munge-0.5.14_1... [main-amd64-default-job-10] | | `-- Extracting munge-0.5.14_1: ......... done ===> Creating groups. Creating group 'slurm' with gid '468'. ===> Creating users Creating user 'slurm' with uid '468'. [main-amd64-default-job-10] | | `-- Extracting slurm-wlm-20.02.7: .......... done [main-amd64-default-job-10] | `-- Extracting mpich-3.4.3: .......... done [main-amd64-default-job-10] `-- Extracting arpack-ng-3.8.0: .......... done [main-amd64-default-job-10] `-- Installing boost-libs-1.72.0_6... [main-amd64-default-job-10] | `-- Installing icu-70.1_1,1... [main-amd64-default-job-10] | `-- Extracting icu-70.1_1,1: .......... done [main-amd64-default-job-10] `-- Extracting boost-libs-1.72.0_6: .......... done [main-amd64-default-job-10] `-- Installing openblas-0.3.18,1... [main-amd64-default-job-10] `-- Extracting openblas-0.3.18,1: .......... done [main-amd64-default-job-10] `-- Installing superlu-5.2.2... [main-amd64-default-job-10] `-- Extracting superlu-5.2.2: .......... done [main-amd64-default-job-10] Extracting armadillo-10.7.1: .......... done ===== Message from slurm-wlm-20.02.7: -- ===> NOTICE: The slurm-wlm port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===== Message from mpich-3.4.3: -- ===> NOTICE: The mpich port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===== Message from boost-libs-1.72.0_6: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===== Message from armadillo-10.7.1: -- ===> NOTICE: The armadillo port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> helfem-g20210912_1 depends on shared library: libarmadillo.so - found (/usr/local/lib/libarmadillo.so) ===> Returning to build of helfem-g20210912_1 ===> helfem-g20210912_1 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.7.pkg [main-amd64-default-job-10] Installing gsl-2.7... [main-amd64-default-job-10] Extracting gsl-2.7: .......... done ===> helfem-g20210912_1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of helfem-g20210912_1 ===> helfem-g20210912_1 depends on shared library: libhdf5_cpp.so - found (/usr/local/lib/libhdf5_cpp.so) ===> helfem-g20210912_1 depends on shared library: libsz.so - found (/usr/local/lib/libsz.so) ===> helfem-g20210912_1 depends on shared library: libxc.so - not found ===> Installing existing package /packages/All/libxc-5.0.0.pkg [main-amd64-default-job-10] Installing libxc-5.0.0... [main-amd64-default-job-10] Extracting libxc-5.0.0: .......... done ===> helfem-g20210912_1 depends on shared library: libxc.so - found (/usr/local/lib/libxc.so) ===> Returning to build of helfem-g20210912_1 =========================================================================== =======================<phase: configure >============================ ===> Configuring for helfem-g20210912_1 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/science/helfem/work/.build ld-elf.so.1: Shared object "libc++.so.1" not found, required by "cmake" *** Error code 1 Stop. make: stopped in /usr/ports/science/helfem