Date: Tue, 5 Feb 2019 16:21:54 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 120armv7-quarterly][science/py-netCDF4] Failed for py36-netCDF4-1.3.1_3 in configure Message-ID: <201902051621.x15GLsxU044909@beefy13.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: gerald@FreeBSD.org Ident: $FreeBSD: branches/2019Q1/science/py-netCDF4/Makefile 487272 2018-12-12 01:35:33Z gerald $ Log URL: http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/492187/logs/py36-netCDF4-1.3.1_3.log Build URL: http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=492187 Log: =>> Building science/py-netCDF4 build started at Tue Feb 5 16:21:17 UTC 2019 port directory: /usr/ports/science/py-netCDF4 package name: py36-netCDF4-1.3.1_3 building for: FreeBSD 120armv7-quarterly-job-23 12.0-RELEASE-p2 FreeBSD 12.0-RELEASE-p2 1200086 arm maintained by: bofh@FreeBSD.org Makefile ident: $FreeBSD: branches/2019Q1/science/py-netCDF4/Makefile 487272 2018-12-12 01:35:33Z gerald $ Poudriere version: 3.2.8 Host OSVERSION: 1300009 Jail OSVERSION: 1200086 Job Id: 23 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RELEASE-p2 1200086 UNAME_r=12.0-RELEASE-p2 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8 MASTERMNT=/usr/local/poudriere/data/.m/120armv7-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/120armv7-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=120armv7-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/120armv7-quarterly/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=py36 DEPENDS_ARGS= MAKE_ARGS= FLAVOR=py36 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for py36-netCDF4-1.3.1_3: 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/python3.6" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-netCDF4/work-py36 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-netCDF4/work-py36 HOME=/wrkdirs/usr/ports/science/py-netCDF4/work-py36 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-netCDF4/work-py36/.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-py36 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-netCDF4/work-py36 HOME=/wrkdirs/usr/ports/science/py-netCDF4/work-py36 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-netCDF4/work-py36/.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 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-- PORTDOCS="" PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=freebsd12 PYTHON_PYOEXTENSION=opt-1.pyc PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py36-netCDF4" EXAMPLESDIR="share/examples/py36-netCDF4" DATADIR="share/py36-netCDF4" WWWDIR="www/py36-netCDF4" ETCDIR="etc/py36-netCDF4" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/py36-netCDF4 DOCSDIR=/usr/local/share/doc/py36-netCDF4 EXAMPLESDIR=/usr/local/share/examples/py36-netCDF4 WWWDIR=/usr/local/www/py36-netCDF4 ETCDIR=/usr/local/etc/py36-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=armv7 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 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-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_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=12.0-RELEASE-p2 OSREL=12.0 OSVERSION=1200086 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=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 >============================ ===> py36-netCDF4-1.3.1_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [120armv7-quarterly-job-23] Installing pkg-1.10.5_5... [120armv7-quarterly-job-23] Extracting pkg-1.10.5_5: .......... done ===> py36-netCDF4-1.3.1_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py36-netCDF4-1.3.1_3 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by py36-netCDF4-1.3.1_3 for building =========================================================================== =======================<phase: checksum >============================ ===> License MIT accepted by the user ===> Fetching all distfiles required by py36-netCDF4-1.3.1_3 for building => SHA256 Checksum OK for Unidata-netcdf4-python-v1.3.1rel_GH0.tar.gz. <snip> [120armv7-quarterly-job-23] `-- Extracting cblas-1.0_10: ......... done [120armv7-quarterly-job-23] `-- Installing lapack-3.5.0_6... [120armv7-quarterly-job-23] `-- Extracting lapack-3.5.0_6: .......... done [120armv7-quarterly-job-23] `-- Installing py36-setuptools-40.6.2... [120armv7-quarterly-job-23] | `-- Installing python36-3.6.7... [120armv7-quarterly-job-23] | | `-- Installing libffi-3.2.1_3... [120armv7-quarterly-job-23] | | `-- Extracting libffi-3.2.1_3: .......... done [120armv7-quarterly-job-23] | | `-- Installing readline-7.0.5... [120armv7-quarterly-job-23] | | `-- Extracting readline-7.0.5: .......... done [120armv7-quarterly-job-23] | `-- Extracting python36-3.6.7: .......... done [120armv7-quarterly-job-23] `-- Extracting py36-setuptools-40.6.2: .......... done [120armv7-quarterly-job-23] `-- Installing suitesparse-5.2.0_2... [120armv7-quarterly-job-23] | `-- Installing metis-5.1.0_6... [120armv7-quarterly-job-23] | `-- Extracting metis-5.1.0_6: .......... done [120armv7-quarterly-job-23] | `-- Installing openblas-0.2.20_7,1... [120armv7-quarterly-job-23] | `-- Extracting openblas-0.2.20_7,1: ......... done [120armv7-quarterly-job-23] `-- Extracting suitesparse-5.2.0_2: .......... done [120armv7-quarterly-job-23] Extracting py36-numpy-1.15.4_1,1: .......... done Message from gcc8-8.2.0_4: 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/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Message from cblas-1.0_10: ===> 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 python36-3.6.7: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== Message from py36-setuptools-40.6.2: ******************************************************************* Only /usr/local/bin/easy_install-3.6 script has been installed since Python 3.6 is not the default Python version. ******************************************************************* Message from metis-5.1.0_6: ===> NOTICE: The metis 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 ===> py36-netCDF4-1.3.1_3 depends on package: py36-numpy>0 - found ===> Returning to build of py36-netCDF4-1.3.1_3 ===> py36-netCDF4-1.3.1_3 depends on file: /usr/local/bin/cython - not found ===> Installing existing package /packages/All/py27-cython-0.29.txz [120armv7-quarterly-job-23] Installing py27-cython-0.29... [120armv7-quarterly-job-23] `-- Installing py27-setuptools-40.6.2... [120armv7-quarterly-job-23] | `-- Installing python27-2.7.15... [120armv7-quarterly-job-23] | `-- Extracting python27-2.7.15: .......... done [120armv7-quarterly-job-23] `-- Extracting py27-setuptools-40.6.2: .......... done [120armv7-quarterly-job-23] Extracting py27-cython-0.29: .......... done Message from python27-2.7.15: =========================================================================== 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 =========================================================================== ===> py36-netCDF4-1.3.1_3 depends on file: /usr/local/bin/cython - found ===> Returning to build of py36-netCDF4-1.3.1_3 ===> py36-netCDF4-1.3.1_3 depends on executable: cython-3.6 - not found ===> Installing existing package /packages/All/py36-cython-0.29.txz [120armv7-quarterly-job-23] Installing py36-cython-0.29... [120armv7-quarterly-job-23] Extracting py36-cython-0.29: .......... done ===> py36-netCDF4-1.3.1_3 depends on executable: cython-3.6 - found ===> Returning to build of py36-netCDF4-1.3.1_3 ===> py36-netCDF4-1.3.1_3 depends on package: py36-setuptools>0 - found ===> py36-netCDF4-1.3.1_3 depends on file: /usr/local/bin/python3.6 - found =========================================================================== =======================<phase: lib-depends >============================ ===> py36-netCDF4-1.3.1_3 depends on shared library: libhdf5.so - not found ===> Installing existing package /packages/All/hdf5-1.10.2_1.txz [120armv7-quarterly-job-23] Installing hdf5-1.10.2_1... [120armv7-quarterly-job-23] `-- Installing hdf-szip-2.1_2... [120armv7-quarterly-job-23] `-- Extracting hdf-szip-2.1_2: .......... done [120armv7-quarterly-job-23] Extracting hdf5-1.10.2_1: .......... done ===> py36-netCDF4-1.3.1_3 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> Returning to build of py36-netCDF4-1.3.1_3 ===> py36-netCDF4-1.3.1_3 depends on shared library: libnetcdf.so - not found ===> Installing existing package /packages/All/netcdf-4.6.1_1.txz [120armv7-quarterly-job-23] Installing netcdf-4.6.1_1... [120armv7-quarterly-job-23] `-- Installing curl-7.62.0... [120armv7-quarterly-job-23] | `-- Installing ca_root_nss-3.42.1... [120armv7-quarterly-job-23] | `-- Extracting ca_root_nss-3.42.1: ........ done [120armv7-quarterly-job-23] | `-- Installing libnghttp2-1.35.1... [120armv7-quarterly-job-23] | `-- Extracting libnghttp2-1.35.1: .......... done [120armv7-quarterly-job-23] `-- Extracting curl-7.62.0: .......... done [120armv7-quarterly-job-23] `-- Installing pkgconf-1.5.4,1... [120armv7-quarterly-job-23] `-- Extracting pkgconf-1.5.4,1: .......... done [120armv7-quarterly-job-23] Extracting netcdf-4.6.1_1: .......... done Message from ca_root_nss-3.42.1: ********************************* 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 *************************************************************************** ===> py36-netCDF4-1.3.1_3 depends on shared library: libnetcdf.so - found (/usr/local/lib/libnetcdf.so) ===> Returning to build of py36-netCDF4-1.3.1_3 =========================================================================== =======================<phase: configure >============================ ===> Configuring for py36-netCDF4-1.3.1_3 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 ... HDF5 library version: 1.10.2 found in None Traceback (most recent call last): File "/usr/local/lib/python3.6/site-packages/numpy/core/__init__.py", line 16, in <module> from . import multiarray ImportError: /usr/local/lib/libblas.so.2: Undefined symbol "__aeabi_uidiv@GCC_3.5" During handling of the above exception, another exception occurred: Traceback (most recent call last): File "<string>", line 1, in <module> File "setup.py", line 458, in <module> import numpy File "/usr/local/lib/python3.6/site-packages/numpy/__init__.py", line 142, in <module> from . import add_newdocs File "/usr/local/lib/python3.6/site-packages/numpy/add_newdocs.py", line 13, in <module> from numpy.lib import add_newdoc File "/usr/local/lib/python3.6/site-packages/numpy/lib/__init__.py", line 8, in <module> from .type_check import * File "/usr/local/lib/python3.6/site-packages/numpy/lib/type_check.py", line 11, in <module> import numpy.core.numeric as _nx File "/usr/local/lib/python3.6/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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