Date: Tue, 14 Nov 2017 03:06:40 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110armv6-quarterly][science/py-netCDF4] Failed for py27-netCDF4-1.2.9 in configure Message-ID: <201711140306.vAE36eN2088617@beefy15.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: bofh@FreeBSD.org Last committer: bofh@FreeBSD.org Ident: $FreeBSD: branches/2017Q4/science/py-netCDF4/Makefile 450200 2017-09-20 13:19:59Z bofh $ Log URL: http://beefy15.nyi.freebsd.org/data/110armv6-quarterly/454158/logs/py27-netCDF4-1.2.9.log Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=110armv6-quarterly&build=454158 Log: ====>> Building science/py-netCDF4 build started at Tue Nov 14 03:06:05 UTC 2017 port directory: /usr/ports/science/py-netCDF4 building for: FreeBSD 110armv6-quarterly-job-23 11.0-RELEASE-p14 FreeBSD 11.0-RELEASE-p14 1100122 arm maintained by: bofh@FreeBSD.org Makefile ident: $FreeBSD: branches/2017Q4/science/py-netCDF4/Makefile 450200 2017-09-20 13:19:59Z bofh $ Poudriere version: 3.1.22 Host OSVERSION: 1200050 Jail OSVERSION: 1100122 Job Id: 23 ---Begin Environment--- POUDRIEREPATH=/usr/local/bin/poudriere LOCALBASE=/usr/local LIBEXECPREFIX=/usr/local/libexec/poudriere SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIERE_VERSION=3.1.22 HOME=/root USER=root SCRIPTPREFIX=/usr/local/share/poudriere MASTERNAME=110armv6-quarterly PWD=/usr/local/poudriere/data/.m/110armv6-quarterly/ref/.p/pool OLDPWD=/ PKGNAME=py27-netCDF4-1.2.9 POUDRIERE_BUILD_TYPE=bulk PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin QEMU_EMULATING=1 MASTERMNT=/usr/local/poudriere/data/.m/110armv6-quarterly/ref SAVED_TERM= STATUS=1 MAIL=/var/mail/root BLOCKSIZE=K UNAME_r=11.0-RELEASE-p14 UNAME_v=FreeBSD 11.0-RELEASE-p14 1100122 OSVERSION=1100122 ABI_FILE=/usr/lib/crt1.o UNAME_m=arm UNAME_p=armv6 SHELL=/bin/csh ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for py27-netCDF4-1.2.9: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-netCDF4/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-netCDF4/work HOME=/wrkdirs/usr/ports/science/py-netCDF4/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-netCDF4/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-netCDF4/work HOME=/wrkdirs/usr/ports/science/py-netCDF4/work TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LDSHARED="/nxb-bin/usr/bin/cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -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-- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd11 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/py-netCDF4" EXAMPLESDIR="share/examples/py-netCDF4" DATADIR="share/netCDF4" WWWDIR="www/netCDF4" ETCDIR="etc/netCDF4" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/netCDF4 DOCSDIR=/usr/local/share/doc/py-netCDF4 EXAMPLESDIR=/usr/local/share/examples/py-netCDF4 WWWDIR=/usr/local/www/netCDF4 ETCDIR=/usr/local/etc/netCDF4 --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 MACHINE=arm MACHINE_ARCH=armv6 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 #### ARCH=armv6 CONFIGURE_MAX_CMD_LEN=262144 OPSYS=FreeBSD OSREL=11.0 OSVERSION=1100122 PYTHONBASE=/usr/local UID=0 _JAVA_OS_LIST_REGEXP=native|linux _JAVA_VENDOR_LIST_REGEXP=openjdk|oracle|sun _JAVA_VERSION_LIST_REGEXP=1.6|1.7|1.8|1.6\+|1.7\+|1.8\+ _OSRELEASE=11.0-RELEASE-p14 #### Misc Poudriere #### GID=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++ AS=/nxb-bin/usr/bin/as 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 MIT accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> py27-netCDF4-1.2.9 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz [110armv6-quarterly-job-23] Installing pkg-1.10.1... [110armv6-quarterly-job-23] Extracting pkg-1.10.1: .......... done ===> py27-netCDF4-1.2.9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py27-netCDF4-1.2.9 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by py27-netCDF4-1.2.9 for building =========================================================================== =======================<phase: checksum >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by py27-netCDF4-1.2.9 for building => SHA256 Checksum OK for Unidata-netcdf4-python-v1.2.9rel_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by py27-netCDF4-1.2.9 for building ===> Extracting for py27-netCDF4-1.2.9 => SHA256 Checksum OK for Unidata-netcdf4-python-v1.2.9rel_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for py27-netCDF4-1.2.9 =========================================================================== =======================<phase: build-depends >============================ ===> py27-netCDF4-1.2.9 depends on file: /usr/local/lib/python2.7/site-packages/numpy/core/numeric.py - not found ===> Installing existing package /packages/All/py27-numpy-1.13.1_2,1.txz [110armv6-quarterly-job-23] Installing py27-numpy-1.13.1_2,1... [110armv6-quarterly-job-23] `-- Installing blas-3.5.0_3... [110armv6-quarterly-job-23] | `-- Installing gcc6-6.4.0_2... [110armv6-quarterly-job-23] | | `-- Installing binutils-2.28,1... [110armv6-quarterly-job-23] | | `-- Installing gettext-runtime-0.19.8.1_1... [110armv6-quarterly-job-23] | | | `-- Installing indexinfo-0.2.6... [110armv6-quarterly-job-23] | | | `-- Extracting indexinfo-0.2.6: .... done [110armv6-quarterly-job-23] | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [110armv6-quarterly-job-23] | | `-- Extracting binutils-2.28,1: .......... done [110armv6-quarterly-job-23] | | `-- Installing gmp-6.1.2... [110armv6-quarterly-job-23] | | `-- Extracting gmp-6.1.2: .......... done [110armv6-quarterly-job-23] | | `-- Installing mpc-1.0.3... [110armv6-quarterly-job-23] | | `-- Installing mpfr-3.1.6... [110armv6-quarterly-job-23] | | `-- Extracting mpfr-3.1.6: .......... done [110armv6-quarterly-job-23] | | `-- Extracting mpc-1.0.3: ...... done [110armv6-quarterly-job-23] | `-- Extracting gcc6-6.4.0_2: .......... done [110armv6-quarterly-job-23] `-- Extracting blas-3.5.0_3: ....... done [110armv6-quarterly-job-23] `-- Installing cblas-1.0_7... [110armv6-quarterly-job-23] `-- Extracting cblas-1.0_7: ......... done [110armv6-quarterly-job-23] `-- Installing lapack-3.5.0_3... [110armv6-quarterly-job-23] `-- Extracting lapack-3.5.0_3: .......... done [110armv6-quarterly-job-23] `-- Installing py27-setuptools-36.2.2... [110armv6-quarterly-job-23] | `-- Installing python27-2.7.14... [110armv6-quarterly-job-23] | | `-- Installing libffi-3.2.1_1... [110armv6-quarterly-job-23] | | `-- Extracting libffi-3.2.1_1: .......... done [110armv6-quarterly-job-23] | | `-- Installing readline-7.0.3... [110armv6-quarterly-job-23] | | `-- Extracting readline-7.0.3: .......... done [110armv6-quarterly-job-23] | `-- Extracting python27-2.7.14: .......... done [110armv6-quarterly-job-23] `-- Extracting py27-setuptools-36.2.2: .......... done [110armv6-quarterly-job-23] `-- Installing suitesparse-4.0.2_7... [110armv6-quarterly-job-23] | `-- Installing openblas-0.2.20_1,1... [110armv6-quarterly-job-23] | `-- Extracting openblas-0.2.20_1,1: ......... done [110armv6-quarterly-job-23] `-- Extracting suitesparse-4.0.2_7: .......... done [110armv6-quarterly-job-23] Extracting py27-numpy-1.13.1_2,1: .......... done Message from gcc6-6.4.0_2: 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/gcc6 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from cblas-1.0_7: ===> NOTICE: The cblas 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Message from python27-2.7.14: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> py27-netCDF4-1.2.9 depends on file: /usr/local/lib/python2.7/site-packages/numpy/core/numeric.py - found ===> Returning to build of py27-netCDF4-1.2.9 ===> py27-netCDF4-1.2.9 depends on file: /usr/local/bin/cython - not found ===> Installing existing package /packages/All/cython-0.26.txz [110armv6-quarterly-job-23] Installing cython-0.26... [110armv6-quarterly-job-23] Extracting cython-0.26: .......... done ===> py27-netCDF4-1.2.9 depends on file: /usr/local/bin/cython - found ===> Returning to build of py27-netCDF4-1.2.9 ===> py27-netCDF4-1.2.9 depends on package: py27-setuptools>0 - found ===> py27-netCDF4-1.2.9 depends on file: /usr/local/bin/python2.7 - found =========================================================================== =======================<phase: lib-depends >============================ ===> py27-netCDF4-1.2.9 depends on shared library: libhdf5.so - not found ===> Installing existing package /packages/All/hdf5-1.10.1_1.txz [110armv6-quarterly-job-23] Installing hdf5-1.10.1_1... [110armv6-quarterly-job-23] `-- Installing hdf-szip-2.1_2... [110armv6-quarterly-job-23] `-- Extracting hdf-szip-2.1_2: ........ done [110armv6-quarterly-job-23] Extracting hdf5-1.10.1_1: .......... done ===> py27-netCDF4-1.2.9 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> Returning to build of py27-netCDF4-1.2.9 ===> py27-netCDF4-1.2.9 depends on shared library: libnetcdf.so - not found ===> Installing existing package /packages/All/netcdf-4.4.1.1_1.txz [110armv6-quarterly-job-23] Installing netcdf-4.4.1.1_1... [110armv6-quarterly-job-23] `-- Installing curl-7.56.1... [110armv6-quarterly-job-23] | `-- Installing ca_root_nss-3.32.1... [110armv6-quarterly-job-23] | `-- Extracting ca_root_nss-3.32.1: ........ done [110armv6-quarterly-job-23] | `-- Installing libnghttp2-1.26.0... [110armv6-quarterly-job-23] | `-- Extracting libnghttp2-1.26.0: .......... done [110armv6-quarterly-job-23] `-- Extracting curl-7.56.1: .......... done [110armv6-quarterly-job-23] `-- Installing pkgconf-1.3.7,1... [110armv6-quarterly-job-23] `-- Extracting pkgconf-1.3.7,1: .......... done [110armv6-quarterly-job-23] Extracting netcdf-4.4.1.1_1: .......... done Message from ca_root_nss-3.32.1: ********************************* WARNING ********************************* 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. *********************************** NOTE ********************************** 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 *************************************************************************** ===> py27-netCDF4-1.2.9 depends on shared library: libnetcdf.so - found (/usr/local/lib/libnetcdf.so) ===> Returning to build of py27-netCDF4-1.2.9 =========================================================================== =======================<phase: configure >============================ ===> Configuring for py27-netCDF4-1.2.9 Package hdf5 was not found in the pkg-config search path. Perhaps you should add the directory containing `hdf5.pc' to the PKG_CONFIG_PATH environment variable Package 'hdf5', required by 'virtual:world', not found reading from setup.cfg... using nc-config ... Traceback (most recent call last): File "<string>", line 1, in <module> File "setup.py", line 368, in <module> import numpy File "/usr/local/lib/python2.7/site-packages/numpy/__init__.py", line 142, in <module> from . import add_newdocs File "/usr/local/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module> from numpy.lib import add_newdoc File "/usr/local/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in <module> from .type_check import * File "/usr/local/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in <module> import numpy.core.numeric as _nx File "/usr/local/lib/python2.7/site-packages/numpy/core/__init__.py", line 26, in <module> raise ImportError(msg) ImportError: Importing the multiarray numpy extension module failed. Most likely you are trying to import a failed build of numpy. If you're working with a numpy git repo, try `git clean -xdf` (removes all files not under version control). Otherwise reinstall numpy. Original error was: /usr/local/lib/gcc6/libgfortran.so.3: Undefined symbol "__aeabi_ldivmod" *** Error code 1 Stop. make: stopped in /usr/ports/science/py-netCDF4
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