[package - head-armv6-default][science/py-netCDF4] Failed for py27-netCDF4-1.3.1_4 in configure

Wed Feb 13 14:02:45 UTC 2019

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 at FreeBSD.org
Last committer: sunpoet at FreeBSD.org
Ident:          $FreeBSD: head/science/py-netCDF4/Makefile 489412 2019-01-05 22:46:53Z sunpoet $
Log URL:        http://beefy8.nyi.freebsd.org/data/head-armv6-default/p492744_s344025/logs/py27-netCDF4-1.3.1_4.log
Build URL:      http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p492744_s344025
Log:

=>> Building science/py-netCDF4
build started at Wed Feb 13 14:01:52 UTC 2019
port directory: /usr/ports/science/py-netCDF4
package name: py27-netCDF4-1.3.1_4
building for: FreeBSD head-armv6-default-job-24 13.0-CURRENT FreeBSD 13.0-CURRENT 1300010 arm
maintained by: bofh at FreeBSD.org
Makefile ident:      $FreeBSD: head/science/py-netCDF4/Makefile 489412 2019-01-05 22:46:53Z sunpoet $
Poudriere version: 3.2.8
Host OSVERSION: 1300009
Jail OSVERSION: 1300010
Job Id: 24

!!! Jail is newer than host. (Jail: 1300010, Host: 1300009) !!!
!!! 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=1300010
UNAME_v=FreeBSD 13.0-CURRENT 1300010
UNAME_r=13.0-CURRENT
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/head-armv6-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=head-armv6-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/head-armv6-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=py27
DEPENDS_ARGS=
MAKE_ARGS= FLAVOR=py27
---End Poudriere Port Flags/Env---

---Begin OPTIONS List---
===> The following configuration options are available for py27-netCDF4-1.3.1_4:
     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 at 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  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/python2.7  PYTHON_LIBDIR=lib/python2.7  PYTHON_PLATFORM=freebsd13  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=13.0 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/py27-netCDF4"  EXAMPLESDIR="share/examples/py27-netCDF4"  DATADIR="share/py27-netCDF4"  WWWDIR="www/py27-netCDF4"  ETCDIR="etc/py27-netCDF4"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/py27-netCDF4 DOCSDIR=/usr/local/share/doc/py27-netCDF4 EXAMPLESDIR=/usr/local/share/examples/py27-netCDF4  WWWDIR=/usr/local/www/py27-netCDF4 ETCDIR=/usr/local/etc/py27-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

# 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 7.0.1 (tags/RELEASE_701/final 349250) (based on LLVM 7.0.1) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
_ALTCCVERSION_9d218390=none
_CXXINTERNAL_9c45a5b1=FreeBSD clang version 7.0.1 (tags/RELEASE_701/final 349250) (based on LLVM 7.0.1) Target: armv6-unknown-freebsd13.0-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 7.0.1 (tags/RELEASE_701/final 349250) (based on LLVM 7.0.1) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
_OBJC_ALTCCVERSION_9d218390=none
ARCH=armv6
OPSYS=FreeBSD
_OSRELEASE=13.0-CURRENT
OSREL=13.0
OSVERSION=1300010
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    >============================
===>   py27-netCDF4-1.3.1_4 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.5_5.txz
[head-armv6-default-job-24] Installing pkg-1.10.5_5...
[head-armv6-default-job-24] Extracting pkg-1.10.5_5: .......... done
===>   py27-netCDF4-1.3.1_4 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of py27-netCDF4-1.3.1_4
===========================================================================
<snip>
=> SHA256 Checksum OK for Unidata-netcdf4-python-v1.3.1rel_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License MIT accepted by the user
===> Fetching all distfiles required by py27-netCDF4-1.3.1_4 for building
===>  Extracting for py27-netCDF4-1.3.1_4
=> SHA256 Checksum OK for Unidata-netcdf4-python-v1.3.1rel_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for py27-netCDF4-1.3.1_4
===========================================================================
=======================<phase: build-depends  >============================
===>   py27-netCDF4-1.3.1_4 depends on package: py27-numpy>0 - not found
===>   Installing existing package /packages/All/py27-numpy-1.15.4_1,1.txz
[head-armv6-default-job-24] Installing py27-numpy-1.15.4_1,1...
[head-armv6-default-job-24] `-- Installing blas-3.5.0_5...
[head-armv6-default-job-24] |   `-- Installing gcc8-8.2.0_4...
[head-armv6-default-job-24] |   | `-- Installing binutils-2.31.1_2,1...
[head-armv6-default-job-24] |   |   `-- Installing gettext-runtime-0.19.8.1_2...
[head-armv6-default-job-24] |   |   | `-- Installing indexinfo-0.3.1...
[head-armv6-default-job-24] |   |   | `-- Extracting indexinfo-0.3.1: .... done
[head-armv6-default-job-24] |   |   `-- Extracting gettext-runtime-0.19.8.1_2: .......... done
[head-armv6-default-job-24] |   | `-- Extracting binutils-2.31.1_2,1: .......... done
[head-armv6-default-job-24] |   | `-- Installing gmp-6.1.2_1...
[head-armv6-default-job-24] |   | `-- Extracting gmp-6.1.2_1: .......... done
[head-armv6-default-job-24] |   | `-- Installing mpc-1.1.0_2...
[head-armv6-default-job-24] |   |   `-- Installing mpfr-4.0.1_2...
[head-armv6-default-job-24] |   |   `-- Extracting mpfr-4.0.1_2: .......... done
[head-armv6-default-job-24] |   | `-- Extracting mpc-1.1.0_2: ......... done
[head-armv6-default-job-24] |   `-- Extracting gcc8-8.2.0_4: .......... done
[head-armv6-default-job-24] `-- Extracting blas-3.5.0_5: ....... done
[head-armv6-default-job-24] `-- Installing cblas-1.0_10...
[head-armv6-default-job-24] `-- Extracting cblas-1.0_10: ......... done
[head-armv6-default-job-24] `-- Installing lapack-3.5.0_6...
[head-armv6-default-job-24] `-- Extracting lapack-3.5.0_6: .......... done
[head-armv6-default-job-24] `-- Installing py27-setuptools-40.8.0...
[head-armv6-default-job-24] |   `-- Installing python27-2.7.15...
[head-armv6-default-job-24] |   | `-- Installing libffi-3.2.1_3...
[head-armv6-default-job-24] |   | `-- Extracting libffi-3.2.1_3: .......... done
[head-armv6-default-job-24] |   | `-- Installing readline-7.0.5...
[head-armv6-default-job-24] |   | `-- Extracting readline-7.0.5: .......... done
[head-armv6-default-job-24] |   `-- Extracting python27-2.7.15: .......... done
[head-armv6-default-job-24] `-- Extracting py27-setuptools-40.8.0: .......... done
[head-armv6-default-job-24] `-- Installing suitesparse-5.2.0_2...
[head-armv6-default-job-24] |   `-- Installing metis-5.1.0_7...
[head-armv6-default-job-24] |   `-- Extracting metis-5.1.0_7: .......... done
[head-armv6-default-job-24] |   `-- Installing openblas-0.2.20_7,1...
[head-armv6-default-job-24] |   `-- Extracting openblas-0.2.20_7,1: ......... done
[head-armv6-default-job-24] `-- Extracting suitesparse-5.2.0_2: .......... done
[head-armv6-default-job-24] Extracting py27-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 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

===========================================================================
Message from metis-5.1.0_7:

===>   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
===>   py27-netCDF4-1.3.1_4 depends on package: py27-numpy>0 - found
===>   Returning to build of py27-netCDF4-1.3.1_4
===>   py27-netCDF4-1.3.1_4 depends on file: /usr/local/bin/cython - not found
===>   Installing existing package /packages/All/py27-cython-0.29.txz
[head-armv6-default-job-24] Installing py27-cython-0.29...
[head-armv6-default-job-24] Extracting py27-cython-0.29: .......... done
===>   py27-netCDF4-1.3.1_4 depends on file: /usr/local/bin/cython - found
===>   Returning to build of py27-netCDF4-1.3.1_4
===>   py27-netCDF4-1.3.1_4 depends on executable: cython-2.7 - found
===>   py27-netCDF4-1.3.1_4 depends on package: py27-setuptools>0 - found
===>   py27-netCDF4-1.3.1_4 depends on file: /usr/local/bin/python2.7 - found
===========================================================================
=======================<phase: lib-depends    >============================
===>   py27-netCDF4-1.3.1_4 depends on shared library: libhdf5.so - not found
===>   Installing existing package /packages/All/hdf5-1.10.4.txz
[head-armv6-default-job-24] Installing hdf5-1.10.4...
[head-armv6-default-job-24] `-- Installing hdf-szip-2.1_3...
[head-armv6-default-job-24] `-- Extracting hdf-szip-2.1_3: .......... done
[head-armv6-default-job-24] Extracting hdf5-1.10.4: .......... done
===>   py27-netCDF4-1.3.1_4 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so)
===>   Returning to build of py27-netCDF4-1.3.1_4
===>   py27-netCDF4-1.3.1_4 depends on shared library: libnetcdf.so - not found
===>   Installing existing package /packages/All/netcdf-4.6.2.txz
[head-armv6-default-job-24] Installing netcdf-4.6.2...
[head-armv6-default-job-24] `-- Installing curl-7.64.0_1...
[head-armv6-default-job-24] |   `-- Installing ca_root_nss-3.42.1...
[head-armv6-default-job-24] |   `-- Extracting ca_root_nss-3.42.1: ........ done
[head-armv6-default-job-24] |   `-- Installing libnghttp2-1.36.0...
[head-armv6-default-job-24] |   `-- Extracting libnghttp2-1.36.0: .......... done
[head-armv6-default-job-24] `-- Extracting curl-7.64.0_1: .......... done
[head-armv6-default-job-24] `-- Installing pkgconf-1.6.0,1...
[head-armv6-default-job-24] `-- Extracting pkgconf-1.6.0,1: .......... done
[head-armv6-default-job-24] Extracting netcdf-4.6.2: .......... 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

***************************************************************************
===>   py27-netCDF4-1.3.1_4 depends on shared library: libnetcdf.so - found (/usr/local/lib/libnetcdf.so)
===>   Returning to build of py27-netCDF4-1.3.1_4
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for py27-netCDF4-1.3.1_4
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: 1.10.4 found in None
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "setup.py", line 458, 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 at GCC_3.5"

*** Error code 1

Stop.
make: stopped in /usr/ports/science/py-netCDF4