Date: Sat, 23 Dec 2017 08:21:20 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-armv6-default][science/py-netCDF4] Failed for py27-netCDF4-1.2.9_1 in configure Message-ID: <201712230821.vBN8LKlw013791@beefy8.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: mat@FreeBSD.org Ident: $FreeBSD: head/science/py-netCDF4/Makefile 455210 2017-11-30 15:50:30Z mat $ Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p456877_s327051/logs/py27-netCDF4-1.2.9_1.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p456877_s327051 Log: =>> Building science/py-netCDF4 build started at Sat Dec 23 08:20:11 UTC 2017 port directory: /usr/ports/science/py-netCDF4 package name: py27-netCDF4-1.2.9_1 building for: FreeBSD head-armv6-default-job-19 12.0-CURRENT FreeBSD 12.0-CURRENT 1200054 arm maintained by: bofh@FreeBSD.org Makefile ident: $FreeBSD: head/science/py-netCDF4/Makefile 455210 2017-11-30 15:50:30Z mat $ Poudriere version: 3.2.3-16-g77e43413 Host OSVERSION: 1200052 Jail OSVERSION: 1200054 Job Id: 19 !!! Jail is newer than host. (Jail: 1200054, Host: 1200052) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1200054 UNAME_v=FreeBSD 12.0-CURRENT 1200054 UNAME_r=12.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref QEMU_EMULATING=1 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk OLDPWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool MASTERNAME=head-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root P_PYTHON_MAJOR_VER=2 POUDRIERE_VERSION=3.2.3-16-g77e43413 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py27 DEPENDS_ARGS= MAKE_ARGS= FLAVOR=py27 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for py27-netCDF4-1.2.9_1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- bofh@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-netCDF4/work-py27 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-netCDF4/work-py27 HOME=/wrkdirs/usr/ports/science/py-netCDF4/work-py27 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-netCDF4/work-py27/.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-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-netCDF4/work-py27 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-netCDF4/work-py27 HOME=/wrkdirs/usr/ports/science/py-netCDF4/work-py27 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-netCDF4/work-py27/.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 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=freebsd12 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=12.0 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 PACKAGE_BUILDING_FLAVORS=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=12.0 OSVERSION=1200054 PYTHONBASE=/usr/local UID=0 _OSRELEASE=12.0-CURRENT #### 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_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.3_1.txz [head-armv6-default-job-19] Installing pkg-1.10.3_1... [head-armv6-default-job-19] Extracting pkg-1.10.3_1: .......... done ===> py27-netCDF4-1.2.9_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py27-netCDF4-1.2.9_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by py27-netCDF4-1.2.9_1 for building =========================================================================== =======================<phase: checksum >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by py27-netCDF4-1.2.9_1 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_1 for building ===> Extracting for py27-netCDF4-1.2.9_1 => 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_1 =========================================================================== =======================<phase: build-depends >============================ ===> py27-netCDF4-1.2.9_1 depends on package: py27-numpy>0 - not found ===> Installing existing package /packages/All/py27-numpy-1.13.3,1.txz [head-armv6-default-job-19] Installing py27-numpy-1.13.3,1... [head-armv6-default-job-19] `-- Installing blas-3.5.0_3... [head-armv6-default-job-19] | `-- Installing gcc6-6.4.0_3... [head-armv6-default-job-19] | | `-- Installing binutils-2.28,1... [head-armv6-default-job-19] | | `-- Installing gettext-runtime-0.19.8.1_1... [head-armv6-default-job-19] | | | `-- Installing indexinfo-0.3.1... [head-armv6-default-job-19] | | | `-- Extracting indexinfo-0.3.1: .... done [head-armv6-default-job-19] | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [head-armv6-default-job-19] | | `-- Extracting binutils-2.28,1: .......... done [head-armv6-default-job-19] | | `-- Installing gmp-6.1.2... [head-armv6-default-job-19] | | `-- Extracting gmp-6.1.2: .......... done [head-armv6-default-job-19] | | `-- Installing mpc-1.0.3... [head-armv6-default-job-19] | | `-- Installing mpfr-3.1.6... [head-armv6-default-job-19] | | `-- Extracting mpfr-3.1.6: .......... done [head-armv6-default-job-19] | | `-- Extracting mpc-1.0.3: ...... done [head-armv6-default-job-19] | `-- Extracting gcc6-6.4.0_3: .......... done [head-armv6-default-job-19] `-- Extracting blas-3.5.0_3: ....... done [head-armv6-default-job-19] `-- Installing cblas-1.0_7... [head-armv6-default-job-19] `-- Extracting cblas-1.0_7: ......... done [head-armv6-default-job-19] `-- Installing lapack-3.5.0_3... [head-armv6-default-job-19] `-- Extracting lapack-3.5.0_3: .......... done [head-armv6-default-job-19] `-- Installing py27-setuptools-36.5.0... [head-armv6-default-job-19] | `-- Installing python27-2.7.14_1... [head-armv6-default-job-19] | | `-- Installing libffi-3.2.1_2... [head-armv6-default-job-19] | | `-- Extracting libffi-3.2.1_2: .......... done [head-armv6-default-job-19] | | `-- Installing readline-7.0.3_1... [head-armv6-default-job-19] | | `-- Extracting readline-7.0.3_1: .......... done [head-armv6-default-job-19] | `-- Extracting python27-2.7.14_1: .......... done [head-armv6-default-job-19] `-- Extracting py27-setuptools-36.5.0: .......... done [head-armv6-default-job-19] `-- Installing suitesparse-4.0.2_7... [head-armv6-default-job-19] | `-- Installing openblas-0.2.20_1,1... [head-armv6-default-job-19] | `-- Extracting openblas-0.2.20_1,1: ......... done [head-armv6-default-job-19] `-- Extracting suitesparse-4.0.2_7: .......... done [head-armv6-default-job-19] Extracting py27-numpy-1.13.3,1: .......... done Message from gcc6-6.4.0_3: 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_1: =========================================================================== 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_1 depends on package: py27-numpy>0 - found ===> Returning to build of py27-netCDF4-1.2.9_1 ===> py27-netCDF4-1.2.9_1 depends on executable: cython-2.7 - not found ===> Installing existing package /packages/All/py27-cython-0.26.txz [head-armv6-default-job-19] Installing py27-cython-0.26... [head-armv6-default-job-19] Extracting py27-cython-0.26: .......... done ===> py27-netCDF4-1.2.9_1 depends on executable: cython-2.7 - found ===> Returning to build of py27-netCDF4-1.2.9_1 ===> py27-netCDF4-1.2.9_1 depends on package: py27-setuptools>0 - found ===> py27-netCDF4-1.2.9_1 depends on file: /usr/local/bin/python2.7 - found =========================================================================== =======================<phase: lib-depends >============================ ===> py27-netCDF4-1.2.9_1 depends on shared library: libhdf5.so - not found ===> Installing existing package /packages/All/hdf5-1.10.1_1.txz [head-armv6-default-job-19] Installing hdf5-1.10.1_1... [head-armv6-default-job-19] `-- Installing hdf-szip-2.1_2... [head-armv6-default-job-19] `-- Extracting hdf-szip-2.1_2: ........ done [head-armv6-default-job-19] Extracting hdf5-1.10.1_1: .......... done ===> py27-netCDF4-1.2.9_1 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> Returning to build of py27-netCDF4-1.2.9_1 ===> py27-netCDF4-1.2.9_1 depends on shared library: libnetcdf.so - not found ===> Installing existing package /packages/All/netcdf-4.5.0.txz [head-armv6-default-job-19] Installing netcdf-4.5.0... [head-armv6-default-job-19] `-- Installing curl-7.57.0... [head-armv6-default-job-19] | `-- Installing ca_root_nss-3.34.1... [head-armv6-default-job-19] | `-- Extracting ca_root_nss-3.34.1: ........ done [head-armv6-default-job-19] | `-- Installing libnghttp2-1.29.0... [head-armv6-default-job-19] | `-- Extracting libnghttp2-1.29.0: .......... done [head-armv6-default-job-19] `-- Extracting curl-7.57.0: .......... done [head-armv6-default-job-19] `-- Installing pkgconf-1.3.10,1... [head-armv6-default-job-19] `-- Extracting pkgconf-1.3.10,1: .......... done [head-armv6-default-job-19] Extracting netcdf-4.5.0: .......... done Message from ca_root_nss-3.34.1: ********************************* 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_1 depends on shared library: libnetcdf.so - found (/usr/local/lib/libnetcdf.so) ===> Returning to build of py27-netCDF4-1.2.9_1 =========================================================================== =======================<phase: configure >============================ ===> Configuring for py27-netCDF4-1.2.9_1 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/libblas.so.2: Undefined symbol "__aeabi_uidiv@GCC_3.5" *** Error code 1 Stop. make: stopped in /usr/ports/science/py-netCDF4
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