[package - 111armv6-quarterly][biology/py-bx-python] Failed for py36-bx-python-0.7.4 in configure

Thu Jan 18 05:01:41 UTC 2018

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 at rawbw.com
Last committer: mat at FreeBSD.org
Ident:          $FreeBSD: branches/2018Q1/biology/py-bx-python/Makefile 455210 2017-11-30 15:50:30Z mat $
Log URL:        http://beefy15.nyi.freebsd.org/data/111armv6-quarterly/459307/logs/py36-bx-python-0.7.4.log
Build URL:      http://beefy15.nyi.freebsd.org/build.html?mastername=111armv6-quarterly&build=459307
Log:

=>> Building biology/py-bx-python
build started at Thu Jan 18 05:01:02 UTC 2018
port directory: /usr/ports/biology/py-bx-python
package name: py36-bx-python-0.7.4
building for: FreeBSD 111armv6-quarterly-job-14 11.1-RELEASE-p6 FreeBSD 11.1-RELEASE-p6 1101001 arm
maintained by: yuri at rawbw.com
Makefile ident:      $FreeBSD: branches/2018Q1/biology/py-bx-python/Makefile 455210 2017-11-30 15:50:30Z mat $
Poudriere version: 3.2.4
Host OSVERSION: 1200054
Jail OSVERSION: 1101001
Job Id: 14

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UNAME_p=armv6
SHELL=/bin/csh
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---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=py36
DEPENDS_ARGS=
MAKE_ARGS= FLAVOR=py36
---End Poudriere Port Flags/Env---

---Begin OPTIONS List---
---End OPTIONS List---

--MAINTAINER--
yuri at rawbw.com
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py36  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py36  HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py36 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-bx-python/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/biology/py-bx-python/work-py36  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py36  HOME=/wrkdirs/usr/ports/biology/py-bx-python/work-py36 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-bx-python/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  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--

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PYTHON_INCLUDEDIR=include/python3.6m  PYTHON_LIBDIR=lib/python3.6  PYTHON_PLATFORM=freebsd11  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=11.1 PREFIX=%D LOCALBASE=/usr/local  RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/bx-python"  EXAMPLESDIR="share/examples/bx-python"  DATADIR="share/bx-python"  WWWDIR="www/bx-python"  ETCDIR="etc/bx-python"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/bx-python DOCSDIR=/usr/local/share/doc/bx-python EXAMPLESDIR=/usr/local/share/examples/bx-python  WWWDIR=/usr/local/www/bx-python ETCDIR=/usr/local/etc/bx-python
--End SUB_LIST--

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WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
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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
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# try the next if the size is mismatched though.
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# 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=11.1
OSVERSION=1101001
PYTHONBASE=/usr/local
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#### Misc Poudriere ####
GID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
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CC=/nxb-bin/usr/bin/cc
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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
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--Resource limits--
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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
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kqueues                         (-k)  unlimited
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--End resource limits--
=======================<phase: check-sanity   >============================
===>  License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   py36-bx-python-0.7.4 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.3_1.txz
[111armv6-quarterly-job-14] Installing pkg-1.10.3_1...
[111armv6-quarterly-job-14] Extracting pkg-1.10.3_1: .......... done
===>   py36-bx-python-0.7.4 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of py36-bx-python-0.7.4
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License MIT accepted by the user
===> Fetching all distfiles required by py36-bx-python-0.7.4 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License MIT accepted by the user
===> Fetching all distfiles required by py36-bx-python-0.7.4 for building
=> SHA256 Checksum OK for bxlab-bx-python-v0.7.4_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License MIT accepted by the user
===> Fetching all distfiles required by py36-bx-python-0.7.4 for building
===>  Extracting for py36-bx-python-0.7.4
=> SHA256 Checksum OK for bxlab-bx-python-v0.7.4_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for py36-bx-python-0.7.4
===========================================================================
=======================<phase: build-depends  >============================
===>   py36-bx-python-0.7.4 depends on package: py36-numpy>0 - not found
===>   Installing existing package /packages/All/py36-numpy-1.13.3,1.txz
[111armv6-quarterly-job-14] Installing py36-numpy-1.13.3,1...
[111armv6-quarterly-job-14] `-- Installing blas-3.5.0_3...
[111armv6-quarterly-job-14] |   `-- Installing gcc6-6.4.0_3...
[111armv6-quarterly-job-14] |   | `-- Installing binutils-2.28,1...
[111armv6-quarterly-job-14] |   |   `-- Installing gettext-runtime-0.19.8.1_1...
[111armv6-quarterly-job-14] |   |   | `-- Installing indexinfo-0.3.1...
[111armv6-quarterly-job-14] |   |   | `-- Extracting indexinfo-0.3.1: .... done
[111armv6-quarterly-job-14] |   |   `-- Extracting gettext-runtime-0.19.8.1_1: .......... done
[111armv6-quarterly-job-14] |   | `-- Extracting binutils-2.28,1: .......... done
[111armv6-quarterly-job-14] |   | `-- Installing gmp-6.1.2...
[111armv6-quarterly-job-14] |   | `-- Extracting gmp-6.1.2: .......... done
[111armv6-quarterly-job-14] |   | `-- Installing mpc-1.0.3...
[111armv6-quarterly-job-14] |   |   `-- Installing mpfr-3.1.6...
[111armv6-quarterly-job-14] |   |   `-- Extracting mpfr-3.1.6: .......... done
[111armv6-quarterly-job-14] |   | `-- Extracting mpc-1.0.3: ...... done
[111armv6-quarterly-job-14] |   `-- Extracting gcc6-6.4.0_3: .......... done
[111armv6-quarterly-job-14] `-- Extracting blas-3.5.0_3: ....... done
[111armv6-quarterly-job-14] `-- Installing cblas-1.0_7...
[111armv6-quarterly-job-14] `-- Extracting cblas-1.0_7: ......... done
[111armv6-quarterly-job-14] `-- Installing lapack-3.5.0_3...
[111armv6-quarterly-job-14] `-- Extracting lapack-3.5.0_3: .......... done
[111armv6-quarterly-job-14] `-- Installing py36-setuptools-36.5.0...
[111armv6-quarterly-job-14] |   `-- Installing python36-3.6.4...
[111armv6-quarterly-job-14] |   | `-- Installing libffi-3.2.1_2...
[111armv6-quarterly-job-14] |   | `-- Extracting libffi-3.2.1_2: .......... done
[111armv6-quarterly-job-14] |   | `-- Installing readline-7.0.3_1...
[111armv6-quarterly-job-14] |   | `-- Extracting readline-7.0.3_1: .......... done
[111armv6-quarterly-job-14] |   `-- Extracting python36-3.6.4: .......... done
[111armv6-quarterly-job-14] `-- Extracting py36-setuptools-36.5.0: .......... done
[111armv6-quarterly-job-14] `-- Installing suitesparse-4.0.2_7...
[111armv6-quarterly-job-14] |   `-- Installing openblas-0.2.20_1,1...
[111armv6-quarterly-job-14] |   `-- Extracting openblas-0.2.20_1,1: ......... done
[111armv6-quarterly-job-14] `-- Extracting suitesparse-4.0.2_7: .......... done
[111armv6-quarterly-job-14] Extracting py36-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 python36-3.6.4:

===========================================================================

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 at py36
py36-sqlite3    databases/py-sqlite3 at py36
py36-tkinter    x11-toolkits/py-tkinter at py36

===========================================================================
Message from py36-setuptools-36.5.0:

*******************************************************************

  Only /usr/local/bin/easy_install-3.6 script has been installed
  since Python 3.6 is not the default Python version.

*******************************************************************
===>   py36-bx-python-0.7.4 depends on package: py36-numpy>0 - found
===>   Returning to build of py36-bx-python-0.7.4
===>   py36-bx-python-0.7.4 depends on package: py36-python-lzo>0 - not found
===>   Installing existing package /packages/All/py36-python-lzo-1.11.txz
[111armv6-quarterly-job-14] Installing py36-python-lzo-1.11...
[111armv6-quarterly-job-14] `-- Installing lzo2-2.10_1...
[111armv6-quarterly-job-14] `-- Extracting lzo2-2.10_1: .......... done
[111armv6-quarterly-job-14] Extracting py36-python-lzo-1.11: ........ done
===>   py36-bx-python-0.7.4 depends on package: py36-python-lzo>0 - found
===>   Returning to build of py36-bx-python-0.7.4
===>   py36-bx-python-0.7.4 depends on package: py36-setuptools>0 - found
===>   py36-bx-python-0.7.4 depends on file: /usr/local/bin/python3.6 - found
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for py36-bx-python-0.7.4
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "setup.py", line 251, in <module>
    main()
  File "setup.py", line 64, in main
    raise Exception( "numpy must be installed to build" )
Exception: numpy must be installed to build
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/py-bx-python