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Date:      Wed, 6 Feb 2019 07:53:58 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 120armv7-quarterly][biology/pycogent] Failed for pycogent-1.9_2 in configure
Message-ID:  <201902060753.x167rwpQ098474@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:     python@FreeBSD.org
Last committer: gerald@FreeBSD.org
Ident:          $FreeBSD: branches/2019Q1/biology/pycogent/Makefile 487272 2018-12-12 01:35:33Z gerald $
Log URL:        http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/492187/logs/pycogent-1.9_2.log
Build URL:      http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=492187
Log:

=>> Building biology/pycogent
build started at Wed Feb  6 07:53:25 UTC 2019
port directory: /usr/ports/biology/pycogent
package name: pycogent-1.9_2
building for: FreeBSD 120armv7-quarterly-job-13 12.0-RELEASE-p2 FreeBSD 12.0-RELEASE-p2 1200086 arm
maintained by: python@FreeBSD.org
Makefile ident:      $FreeBSD: branches/2019Q1/biology/pycogent/Makefile 487272 2018-12-12 01:35:33Z gerald $
Poudriere version: 3.2.8
Host OSVERSION: 1300009
Jail OSVERSION: 1200086
Job Id: 13

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python@FreeBSD.org
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--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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--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/pycogent DOCSDIR=/usr/local/share/doc/pycogent EXAMPLESDIR=/usr/local/share/examples/pycogent  WWWDIR=/usr/local/www/pycogent ETCDIR=/usr/local/etc/pycogent
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ARCH=${MACHINE_ARCH}
#### /usr/local/etc/poudriere.d/make.conf ####
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CC_OUTPUT_9d218390_67d20829=yes
CC_OUTPUT_9d218390_bfa62e83=yes
CC_OUTPUT_9d218390_f0b4d593=yes
CC_OUTPUT_9d218390_308abb44=yes
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UID=0
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--Resource limits--
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data seg size           (kbytes, -d)  33554432
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max user processes              (-u)  89999
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swap limit              (kbytes, -w)  unlimited
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umtx shared locks               (-o)  unlimited
--End resource limits--
=======================<phase: check-sanity   >============================
===>  License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   pycogent-1.9_2 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.5_5.txz
[120armv7-quarterly-job-13] Installing pkg-1.10.5_5...
[120armv7-quarterly-job-13] Extracting pkg-1.10.5_5: .......... done
===>   pycogent-1.9_2 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of pycogent-1.9_2
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by pycogent-1.9_2 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License GPLv2 accepted by the user
===> Fetching all distfiles required by pycogent-1.9_2 for building
=> SHA256 Checksum OK for pycogent-pycogent-1.9_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
<snip>
[120armv7-quarterly-job-13] |   | `-- Extracting gmp-6.1.2_1: .......... done
[120armv7-quarterly-job-13] |   | `-- Installing mpc-1.1.0_2...
[120armv7-quarterly-job-13] |   |   `-- Installing mpfr-4.0.1_2...
[120armv7-quarterly-job-13] |   |   `-- Extracting mpfr-4.0.1_2: .......... done
[120armv7-quarterly-job-13] |   | `-- Extracting mpc-1.1.0_2: ......... done
[120armv7-quarterly-job-13] |   `-- Extracting gcc8-8.2.0_4: .......... done
[120armv7-quarterly-job-13] `-- Extracting blas-3.5.0_5: ....... done
[120armv7-quarterly-job-13] `-- Installing cblas-1.0_10...
[120armv7-quarterly-job-13] `-- Extracting cblas-1.0_10: ......... done
[120armv7-quarterly-job-13] `-- Installing lapack-3.5.0_6...
[120armv7-quarterly-job-13] `-- Extracting lapack-3.5.0_6: .......... done
[120armv7-quarterly-job-13] `-- Installing py27-setuptools-40.6.2...
[120armv7-quarterly-job-13] |   `-- Installing python27-2.7.15...
[120armv7-quarterly-job-13] |   | `-- Installing libffi-3.2.1_3...
[120armv7-quarterly-job-13] |   | `-- Extracting libffi-3.2.1_3: .......... done
[120armv7-quarterly-job-13] |   | `-- Installing readline-7.0.5...
[120armv7-quarterly-job-13] |   | `-- Extracting readline-7.0.5: .......... done
[120armv7-quarterly-job-13] |   `-- Extracting python27-2.7.15: .......... done
[120armv7-quarterly-job-13] `-- Extracting py27-setuptools-40.6.2: .......... done
[120armv7-quarterly-job-13] `-- Installing suitesparse-5.2.0_2...
[120armv7-quarterly-job-13] |   `-- Installing metis-5.1.0_6...
[120armv7-quarterly-job-13] |   `-- Extracting metis-5.1.0_6: .......... done
[120armv7-quarterly-job-13] |   `-- Installing openblas-0.2.20_7,1...
[120armv7-quarterly-job-13] |   `-- Extracting openblas-0.2.20_7,1: ......... done
[120armv7-quarterly-job-13] `-- Extracting suitesparse-5.2.0_2: .......... done
[120armv7-quarterly-job-13] 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_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
===>   pycogent-1.9_2 depends on package: py27-numpy>0 - found
===>   Returning to build of pycogent-1.9_2
===>   pycogent-1.9_2 depends on package: py27-sphinx>=0 - not found
===>   Installing existing package /packages/All/py27-sphinx-1.6.5_1,1.txz
[120armv7-quarterly-job-13] Installing py27-sphinx-1.6.5_1,1...
[120armv7-quarterly-job-13] `-- Installing ca_root_nss-3.42.1...
[120armv7-quarterly-job-13] `-- Extracting ca_root_nss-3.42.1: ........ done
[120armv7-quarterly-job-13] `-- Installing py27-Babel-2.6.0...
[120armv7-quarterly-job-13] |   `-- Installing py27-pytz-2018.7,1...
[120armv7-quarterly-job-13] |   `-- Extracting py27-pytz-2018.7,1: .......... done
[120armv7-quarterly-job-13] `-- Extracting py27-Babel-2.6.0: .......... done
[120armv7-quarterly-job-13] `-- Installing py27-Jinja2-2.10...
[120armv7-quarterly-job-13] |   `-- Installing py27-MarkupSafe-1.0...
[120armv7-quarterly-job-13] |   `-- Extracting py27-MarkupSafe-1.0: .......... done
[120armv7-quarterly-job-13] `-- Extracting py27-Jinja2-2.10: .......... done
[120armv7-quarterly-job-13] `-- Installing py27-alabaster-0.7.6...
[120armv7-quarterly-job-13] `-- Extracting py27-alabaster-0.7.6: .......... done
[120armv7-quarterly-job-13] `-- Installing py27-docutils-0.14_3...
[120armv7-quarterly-job-13] `-- Extracting py27-docutils-0.14_3: .......... done
[120armv7-quarterly-job-13] `-- Installing py27-imagesize-0.7.1...
[120armv7-quarterly-job-13] `-- Extracting py27-imagesize-0.7.1: .......... done
[120armv7-quarterly-job-13] `-- Installing py27-pygments-2.3.0...
[120armv7-quarterly-job-13] `-- Extracting py27-pygments-2.3.0: .......... done
[120armv7-quarterly-job-13] `-- Installing py27-requests-2.18.4_1...
[120armv7-quarterly-job-13] |   `-- Installing py27-certifi-2018.11.29...
[120armv7-quarterly-job-13] |   `-- Extracting py27-certifi-2018.11.29: .......... done
[120armv7-quarterly-job-13] |   `-- Installing py27-chardet-3.0.4...
[120armv7-quarterly-job-13] |   `-- Extracting py27-chardet-3.0.4: .......... done
[120armv7-quarterly-job-13] |   `-- Installing py27-idna-2.7...
[120armv7-quarterly-job-13] |   `-- Extracting py27-idna-2.7: .......... done
[120armv7-quarterly-job-13] |   `-- Installing py27-urllib3-1.22,1...
[120armv7-quarterly-job-13] |   | `-- Installing py27-cryptography-2.3...
[120armv7-quarterly-job-13] |   |   `-- Installing py27-asn1crypto-0.22.0...
[120armv7-quarterly-job-13] |   |   `-- Extracting py27-asn1crypto-0.22.0: .......... done
[120armv7-quarterly-job-13] |   |   `-- Installing py27-cffi-1.11.5...
[120armv7-quarterly-job-13] |   |   | `-- Installing py27-pycparser-2.18...
[120armv7-quarterly-job-13] |   |   | `-- Extracting py27-pycparser-2.18: .......... done
[120armv7-quarterly-job-13] |   |   `-- Extracting py27-cffi-1.11.5: .......... done
[120armv7-quarterly-job-13] |   |   `-- Installing py27-enum34-1.1.6...
[120armv7-quarterly-job-13] |   |   `-- Extracting py27-enum34-1.1.6: .......... done
[120armv7-quarterly-job-13] |   |   `-- Installing py27-ipaddress-1.0.22...
[120armv7-quarterly-job-13] |   |   `-- Extracting py27-ipaddress-1.0.22: .......... done
[120armv7-quarterly-job-13] |   |   `-- Installing py27-six-1.12.0...
[120armv7-quarterly-job-13] |   |   `-- Extracting py27-six-1.12.0: .......... done
[120armv7-quarterly-job-13] |   | `-- Extracting py27-cryptography-2.3: .......... done
[120armv7-quarterly-job-13] |   | `-- Installing py27-openssl-18.0.0...
[120armv7-quarterly-job-13] |   | `-- Extracting py27-openssl-18.0.0: .......... done
[120armv7-quarterly-job-13] |   | `-- Installing py27-pysocks-1.6.8...
[120armv7-quarterly-job-13] |   | `-- Extracting py27-pysocks-1.6.8: .......... done
[120armv7-quarterly-job-13] |   `-- Extracting py27-urllib3-1.22,1: .......... done
[120armv7-quarterly-job-13] `-- Extracting py27-requests-2.18.4_1: .......... done
[120armv7-quarterly-job-13] `-- Installing py27-snowballstemmer-1.2.0_1...
[120armv7-quarterly-job-13] |   `-- Installing py27-pystemmer-1.3.0_2...
[120armv7-quarterly-job-13] |   `-- Extracting py27-pystemmer-1.3.0_2: ......... done
[120armv7-quarterly-job-13] `-- Extracting py27-snowballstemmer-1.2.0_1: .......... done
[120armv7-quarterly-job-13] `-- Installing py27-sphinx_rtd_theme-0.4.2...
[120armv7-quarterly-job-13] `-- Extracting py27-sphinx_rtd_theme-0.4.2: .......... done
[120armv7-quarterly-job-13] `-- Installing py27-sphinxcontrib-websupport-1.0.1...
[120armv7-quarterly-job-13] `-- Extracting py27-sphinxcontrib-websupport-1.0.1: .......... done
[120armv7-quarterly-job-13] `-- Installing py27-typing-3.6.4...
[120armv7-quarterly-job-13] `-- Extracting py27-typing-3.6.4: .......... done
[120armv7-quarterly-job-13] Extracting py27-sphinx-1.6.5_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

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

Be careful, support of IPv6 is broken with PySocks 1.5.7.
===>   pycogent-1.9_2 depends on package: py27-sphinx>=0 - found
===>   Returning to build of pycogent-1.9_2
===>   pycogent-1.9_2 depends on package: py27-sqlalchemy10>=1.0.13 - not found
===>   Installing existing package /packages/All/py27-sqlalchemy10-1.0.14.txz
[120armv7-quarterly-job-13] Installing py27-sqlalchemy10-1.0.14...
[120armv7-quarterly-job-13] `-- Installing py27-sqlite3-2.7.15_7...
[120armv7-quarterly-job-13] |   `-- Installing sqlite3-3.26.0...
[120armv7-quarterly-job-13] |   `-- Extracting sqlite3-3.26.0: .......... done
[120armv7-quarterly-job-13] `-- Extracting py27-sqlite3-2.7.15_7: ........ done
[120armv7-quarterly-job-13] Extracting py27-sqlalchemy10-1.0.14: .......... done
===>   pycogent-1.9_2 depends on package: py27-sqlalchemy10>=1.0.13 - found
===>   Returning to build of pycogent-1.9_2
===>   pycogent-1.9_2 depends on executable: cython-2.7 - not found
===>   Installing existing package /packages/All/py27-cython-0.29.txz
[120armv7-quarterly-job-13] Installing py27-cython-0.29...
[120armv7-quarterly-job-13] Extracting py27-cython-0.29: .......... done
===>   pycogent-1.9_2 depends on executable: cython-2.7 - found
===>   Returning to build of pycogent-1.9_2
===>   pycogent-1.9_2 depends on package: py27-setuptools>0 - found
===>   pycogent-1.9_2 depends on file: /usr/local/bin/python2.7 - found
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for pycogent-1.9_2
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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