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Date:      Thu, 6 Sep 2018 01:38:02 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - head-armv6-default][biology/pycogent] Failed for pycogent-1.9_1 in configure
Message-ID:  <201809060138.w861c2bL043451@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:     python@FreeBSD.org
Last committer: mat@FreeBSD.org
Ident:          $FreeBSD: head/biology/pycogent/Makefile 472884 2018-06-20 17:05:41Z mat $
Log URL:        http://beefy8.nyi.freebsd.org/data/head-armv6-default/p478648_s338416/logs/pycogent-1.9_1.log
Build URL:      http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p478648_s338416
Log:

=>> Building biology/pycogent
build started at Thu Sep  6 01:36:42 UTC 2018
port directory: /usr/ports/biology/pycogent
package name: pycogent-1.9_1
building for: FreeBSD head-armv6-default-job-15 12.0-ALPHA4 FreeBSD 12.0-ALPHA4 1200083 arm
maintained by: python@FreeBSD.org
Makefile ident:      $FreeBSD: head/biology/pycogent/Makefile 472884 2018-06-20 17:05:41Z mat $
Poudriere version: 3.2.7-6-g819c79a1
Host OSVERSION: 1200069
Jail OSVERSION: 1200083
Job Id: 15




!!! Jail is newer than host. (Jail: 1200083, Host: 1200069) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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PKGENV=
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DEPENDS_ARGS=
MAKE_ARGS= FLAVOR=py27
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python@FreeBSD.org
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--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/pycogent/work-py27  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/pycogent/work-py27  HOME=/wrkdirs/usr/ports/biology/pycogent/work-py27 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/pycogent/work-py27/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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--PLIST_SUB--
PORTDOCS="" PORTEXAMPLES="" 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 LIB32DIR=lib DOCSDIR="share/doc/pycogent"  EXAMPLESDIR="share/examples/pycogent"  DATADIR="share/pycogent"  WWWDIR="www/pycogent"  ETCDIR="etc/pycogent"
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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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# Disable build of llib now that head no longer has lint(1)
LINT=	true
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#### /usr/ports/Mk/Scripts/ports_env.sh ####
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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
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OPSYS=FreeBSD
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#### Misc Poudriere ####
GID=0
UID=0
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---End make.conf---
---Begin make.nxb.conf---
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CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
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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 GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   pycogent-1.9_1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.5_2.txz
[head-armv6-default-job-15] Installing pkg-1.10.5_2...
[head-armv6-default-job-15] Extracting pkg-1.10.5_2: .......... done
===>   pycogent-1.9_1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of pycogent-1.9_1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv2 accepted by the user
<snip>
[head-armv6-default-job-15] |   | `-- Extracting gmp-6.1.2: .......... done
[head-armv6-default-job-15] |   | `-- Installing mpc-1.1.0_1...
[head-armv6-default-job-15] |   |   `-- Installing mpfr-4.0.1...
[head-armv6-default-job-15] |   |   `-- Extracting mpfr-4.0.1: .......... done
[head-armv6-default-job-15] |   | `-- Extracting mpc-1.1.0_1: ......... done
[head-armv6-default-job-15] |   `-- Extracting gcc7-7.3.0_5: .......... done
[head-armv6-default-job-15] `-- Extracting blas-3.5.0_4: ....... done
[head-armv6-default-job-15] `-- Installing cblas-1.0_9...
[head-armv6-default-job-15] `-- Extracting cblas-1.0_9: ......... done
[head-armv6-default-job-15] `-- Installing lapack-3.5.0_5...
[head-armv6-default-job-15] `-- Extracting lapack-3.5.0_5: .......... done
[head-armv6-default-job-15] `-- Installing py27-setuptools-40.0.0...
[head-armv6-default-job-15] |   `-- Installing python27-2.7.15...
[head-armv6-default-job-15] |   | `-- Installing libffi-3.2.1_2...
[head-armv6-default-job-15] |   | `-- Extracting libffi-3.2.1_2: .......... done
[head-armv6-default-job-15] |   | `-- Installing readline-7.0.3_1...
[head-armv6-default-job-15] |   | `-- Extracting readline-7.0.3_1: .......... done
[head-armv6-default-job-15] |   `-- Extracting python27-2.7.15: .......... done
[head-armv6-default-job-15] `-- Extracting py27-setuptools-40.0.0: .......... done
[head-armv6-default-job-15] `-- Installing suitesparse-5.2.0_1...
[head-armv6-default-job-15] |   `-- Installing metis-5.1.0_5...
[head-armv6-default-job-15] |   `-- Extracting metis-5.1.0_5: .......... done
[head-armv6-default-job-15] |   `-- Installing openblas-0.2.20_3,1...
[head-armv6-default-job-15] |   `-- Extracting openblas-0.2.20_3,1: ......... done
[head-armv6-default-job-15] `-- Extracting suitesparse-5.2.0_1: .......... done
[head-armv6-default-job-15] Extracting py27-numpy-1.15.0,1: .......... done
Message from gcc7-7.3.0_5:

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/gcc7

For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
Message from cblas-1.0_9:

===>   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_5:

===>   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
===>   pycogent-1.9_1 depends on package: py27-numpy>0 - found
===>   Returning to build of pycogent-1.9_1
===>   pycogent-1.9_1 depends on package: py27-sphinx>=0 - not found
===>   Installing existing package /packages/All/py27-sphinx-1.6.5_1,1.txz
[head-armv6-default-job-15] Installing py27-sphinx-1.6.5_1,1...
[head-armv6-default-job-15] `-- Installing ca_root_nss-3.39...
[head-armv6-default-job-15] `-- Extracting ca_root_nss-3.39: ........ done
[head-armv6-default-job-15] `-- Installing py27-Babel-2.6.0...
[head-armv6-default-job-15] |   `-- Installing py27-pytz-2018.5,1...
[head-armv6-default-job-15] |   `-- Extracting py27-pytz-2018.5,1: .......... done
[head-armv6-default-job-15] `-- Extracting py27-Babel-2.6.0: .......... done
[head-armv6-default-job-15] `-- Installing py27-Jinja2-2.10...
[head-armv6-default-job-15] |   `-- Installing py27-MarkupSafe-1.0...
[head-armv6-default-job-15] |   `-- Extracting py27-MarkupSafe-1.0: .......... done
[head-armv6-default-job-15] `-- Extracting py27-Jinja2-2.10: .......... done
[head-armv6-default-job-15] `-- Installing py27-alabaster-0.7.6...
[head-armv6-default-job-15] `-- Extracting py27-alabaster-0.7.6: .......... done
[head-armv6-default-job-15] `-- Installing py27-docutils-0.14_3...
[head-armv6-default-job-15] `-- Extracting py27-docutils-0.14_3: .......... done
[head-armv6-default-job-15] `-- Installing py27-imagesize-0.7.1...
[head-armv6-default-job-15] `-- Extracting py27-imagesize-0.7.1: .......... done
[head-armv6-default-job-15] `-- Installing py27-pygments-2.2.0...
[head-armv6-default-job-15] `-- Extracting py27-pygments-2.2.0: .......... done
[head-armv6-default-job-15] `-- Installing py27-requests-2.18.4_1...
[head-armv6-default-job-15] |   `-- Installing py27-certifi-2018.4.16...
[head-armv6-default-job-15] |   `-- Extracting py27-certifi-2018.4.16: .......... done
[head-armv6-default-job-15] |   `-- Installing py27-chardet-3.0.4...
[head-armv6-default-job-15] |   `-- Extracting py27-chardet-3.0.4: .......... done
[head-armv6-default-job-15] |   `-- Installing py27-idna-2.7...
[head-armv6-default-job-15] |   `-- Extracting py27-idna-2.7: .......... done
[head-armv6-default-job-15] |   `-- Installing py27-urllib3-1.22,1...
[head-armv6-default-job-15] |   | `-- Installing py27-cryptography-2.3...
[head-armv6-default-job-15] |   |   `-- Installing py27-asn1crypto-0.22.0...
[head-armv6-default-job-15] |   |   `-- Extracting py27-asn1crypto-0.22.0: .......... done
[head-armv6-default-job-15] |   |   `-- Installing py27-cffi-1.11.5...
[head-armv6-default-job-15] |   |   | `-- Installing py27-pycparser-2.18...
[head-armv6-default-job-15] |   |   | `-- Extracting py27-pycparser-2.18: .......... done
[head-armv6-default-job-15] |   |   `-- Extracting py27-cffi-1.11.5: .......... done
[head-armv6-default-job-15] |   |   `-- Installing py27-enum34-1.1.6...
[head-armv6-default-job-15] |   |   `-- Extracting py27-enum34-1.1.6: .......... done
[head-armv6-default-job-15] |   |   `-- Installing py27-ipaddress-1.0.22...
[head-armv6-default-job-15] |   |   `-- Extracting py27-ipaddress-1.0.22: .......... done
[head-armv6-default-job-15] |   |   `-- Installing py27-six-1.11.0...
[head-armv6-default-job-15] |   |   `-- Extracting py27-six-1.11.0: .......... done
[head-armv6-default-job-15] |   | `-- Extracting py27-cryptography-2.3: .......... done
[head-armv6-default-job-15] |   | `-- Installing py27-openssl-17.5.0_1...
[head-armv6-default-job-15] |   | `-- Extracting py27-openssl-17.5.0_1: .......... done
[head-armv6-default-job-15] |   | `-- Installing py27-pysocks-1.6.8...
[head-armv6-default-job-15] |   | `-- Extracting py27-pysocks-1.6.8: .......... done
[head-armv6-default-job-15] |   `-- Extracting py27-urllib3-1.22,1: .......... done
[head-armv6-default-job-15] `-- Extracting py27-requests-2.18.4_1: .......... done
[head-armv6-default-job-15] `-- Installing py27-snowballstemmer-1.2.0_1...
[head-armv6-default-job-15] |   `-- Installing py27-pystemmer-1.3.0_2...
[head-armv6-default-job-15] |   `-- Extracting py27-pystemmer-1.3.0_2: ......... done
[head-armv6-default-job-15] `-- Extracting py27-snowballstemmer-1.2.0_1: .......... done
[head-armv6-default-job-15] `-- Installing py27-sphinx_rtd_theme-0.4.0...
[head-armv6-default-job-15] `-- Extracting py27-sphinx_rtd_theme-0.4.0: .......... done
[head-armv6-default-job-15] `-- Installing py27-sphinxcontrib-websupport-1.0.1...
[head-armv6-default-job-15] `-- Extracting py27-sphinxcontrib-websupport-1.0.1: .......... done
[head-armv6-default-job-15] `-- Installing py27-typing-3.6.4...
[head-armv6-default-job-15] `-- Extracting py27-typing-3.6.4: .......... done
[head-armv6-default-job-15] Extracting py27-sphinx-1.6.5_1,1: .......... done
Message from ca_root_nss-3.39:

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

***************************************************************************
Message from py27-urllib3-1.22,1:

Be careful, support of IPv6 is broken with PySocks 1.5.7.
===>   pycogent-1.9_1 depends on package: py27-sphinx>=0 - found
===>   Returning to build of pycogent-1.9_1
===>   pycogent-1.9_1 depends on package: py27-sqlalchemy10>=1.0.13 - not found
===>   Installing existing package /packages/All/py27-sqlalchemy10-1.0.14.txz
[head-armv6-default-job-15] Installing py27-sqlalchemy10-1.0.14...
[head-armv6-default-job-15] `-- Installing py27-sqlite3-2.7.15_7...
[head-armv6-default-job-15] |   `-- Installing sqlite3-3.24.0_1...
[head-armv6-default-job-15] |   `-- Extracting sqlite3-3.24.0_1: .......... done
[head-armv6-default-job-15] `-- Extracting py27-sqlite3-2.7.15_7: ........ done
[head-armv6-default-job-15] Extracting py27-sqlalchemy10-1.0.14: .......... done
===>   pycogent-1.9_1 depends on package: py27-sqlalchemy10>=1.0.13 - found
===>   Returning to build of pycogent-1.9_1
===>   pycogent-1.9_1 depends on executable: cython-2.7 - not found
===>   Installing existing package /packages/All/py27-cython-0.28.2.txz
[head-armv6-default-job-15] Installing py27-cython-0.28.2...
[head-armv6-default-job-15] Extracting py27-cython-0.28.2: .......... done
===>   pycogent-1.9_1 depends on executable: cython-2.7 - found
===>   Returning to build of pycogent-1.9_1
===>   pycogent-1.9_1 depends on package: py27-setuptools>0 - found
===>   pycogent-1.9_1 depends on file: /usr/local/bin/python2.7 - found
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for pycogent-1.9_1
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "setup.py", line 26, in <module>
    raise RuntimeError("Numpy required but not found.")
RuntimeError: Numpy required but not found.
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/pycogent



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