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Date:      Mon, 1 Apr 2019 10:36:24 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 120armv7-quarterly][biology/py-macs2] Failed for py27-macs2-2.1.0.p20170505_2 in configure
Message-ID:  <201904011036.x31AaOrV020084@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:     jwb@FreeBSD.org
Last committer: gerald@FreeBSD.org
Ident:          $FreeBSD: branches/2019Q1/biology/py-macs2/Makefile 487272 2018-12-12 01:35:33Z gerald $
Log URL:        http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/497364/logs/py27-macs2-2.1.0.p20170505_2.log
Build URL:      http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=497364
Log:

=>> Building biology/py-macs2
build started at Mon Apr  1 10:35:55 UTC 2019
port directory: /usr/ports/biology/py-macs2
package name: py27-macs2-2.1.0.p20170505_2
building for: FreeBSD 120armv7-quarterly-job-02 12.0-RELEASE-p3 FreeBSD 12.0-RELEASE-p3 1200086 arm
maintained by: jwb@FreeBSD.org
Makefile ident:      $FreeBSD: branches/2019Q1/biology/py-macs2/Makefile 487272 2018-12-12 01:35:33Z gerald $
Poudriere version: 3.2.8-3-g02cc9753
Host OSVERSION: 1300009
Jail OSVERSION: 1200086
Job Id: 02

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PKGENV=
FLAVOR=py27
DEPENDS_ARGS=
MAKE_ARGS= FLAVOR=py27
---End Poudriere Port Flags/Env---

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

--MAINTAINER--
jwb@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py27  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py27  HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py27 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-macs2/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/biology/py-macs2/work-py27  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py27  HOME=/wrkdirs/usr/ports/biology/py-macs2/work-py27 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-macs2/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--
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--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/py27-macs2 DOCSDIR=/usr/local/share/doc/py27-macs2 EXAMPLESDIR=/usr/local/share/examples/py27-macs2  WWWDIR=/usr/local/www/py27-macs2 ETCDIR=/usr/local/etc/py27-macs2
--End SUB_LIST--

---Begin make.conf---
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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
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# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
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MAKE_JOBS_NUMBER=2

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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
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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
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ARCH=armv7
OPSYS=FreeBSD
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OSREL=12.0
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GID=0
UID=0
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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
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---End make.nxb.conf---
--Resource limits--
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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 BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   py27-macs2-2.1.0.p20170505_2 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.5_5.txz
[120armv7-quarterly-job-02] Installing pkg-1.10.5_5...
[120armv7-quarterly-job-02] Extracting pkg-1.10.5_5: .......... done
===>   py27-macs2-2.1.0.p20170505_2 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of py27-macs2-2.1.0.p20170505_2
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py27-macs2-2.1.0.p20170505_2 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py27-macs2-2.1.0.p20170505_2 for building
=> SHA256 Checksum OK for taoliu-MACS-2.1.0.p20170505-6946b2f_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py27-macs2-2.1.0.p20170505_2 for building
===>  Extracting for py27-macs2-2.1.0.p20170505_2
=> SHA256 Checksum OK for taoliu-MACS-2.1.0.p20170505-6946b2f_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for py27-macs2-2.1.0.p20170505_2
===========================================================================
=======================<phase: build-depends  >============================
===>   py27-macs2-2.1.0.p20170505_2 depends on package: py27-numpy>0 - not found
===>   Installing existing package /packages/All/py27-numpy-1.15.4_1,1.txz
[120armv7-quarterly-job-02] Installing py27-numpy-1.15.4_1,1...
[120armv7-quarterly-job-02] `-- Installing blas-3.5.0_5...
[120armv7-quarterly-job-02] |   `-- Installing gcc8-8.2.0_4...
[120armv7-quarterly-job-02] |   | `-- Installing binutils-2.30_7,1...
[120armv7-quarterly-job-02] |   |   `-- Installing gettext-runtime-0.19.8.1_2...
[120armv7-quarterly-job-02] |   |   | `-- Installing indexinfo-0.3.1...
[120armv7-quarterly-job-02] |   |   | `-- Extracting indexinfo-0.3.1: .... done
[120armv7-quarterly-job-02] |   |   `-- Extracting gettext-runtime-0.19.8.1_2: .......... done
[120armv7-quarterly-job-02] |   | `-- Extracting binutils-2.30_7,1: .......... done
[120armv7-quarterly-job-02] |   | `-- Installing gmp-6.1.2_1...
[120armv7-quarterly-job-02] |   | `-- Extracting gmp-6.1.2_1: .......... done
[120armv7-quarterly-job-02] |   | `-- Installing mpc-1.1.0_2...
[120armv7-quarterly-job-02] |   |   `-- Installing mpfr-4.0.1_2...
[120armv7-quarterly-job-02] |   |   `-- Extracting mpfr-4.0.1_2: .......... done
[120armv7-quarterly-job-02] |   | `-- Extracting mpc-1.1.0_2: ......... done
[120armv7-quarterly-job-02] |   `-- Extracting gcc8-8.2.0_4: .......... done
[120armv7-quarterly-job-02] `-- Extracting blas-3.5.0_5: ....... done
[120armv7-quarterly-job-02] `-- Installing cblas-1.0_10...
[120armv7-quarterly-job-02] `-- Extracting cblas-1.0_10: ......... done
[120armv7-quarterly-job-02] `-- Installing lapack-3.5.0_6...
[120armv7-quarterly-job-02] `-- Extracting lapack-3.5.0_6: .......... done
[120armv7-quarterly-job-02] `-- Installing py27-setuptools-40.6.2...
[120armv7-quarterly-job-02] |   `-- Installing python27-2.7.15...
[120armv7-quarterly-job-02] |   | `-- Installing libffi-3.2.1_3...
[120armv7-quarterly-job-02] |   | `-- Extracting libffi-3.2.1_3: .......... done
[120armv7-quarterly-job-02] |   | `-- Installing readline-7.0.5...
[120armv7-quarterly-job-02] |   | `-- Extracting readline-7.0.5: .......... done
[120armv7-quarterly-job-02] |   `-- Extracting python27-2.7.15: .......... done
[120armv7-quarterly-job-02] `-- Extracting py27-setuptools-40.6.2: .......... done
[120armv7-quarterly-job-02] `-- Installing suitesparse-5.2.0_2...
[120armv7-quarterly-job-02] |   `-- Installing metis-5.1.0_6...
[120armv7-quarterly-job-02] |   `-- Extracting metis-5.1.0_6: .......... done
[120armv7-quarterly-job-02] |   `-- Installing openblas-0.2.20_7,1...
[120armv7-quarterly-job-02] |   `-- Extracting openblas-0.2.20_7,1: ......... done
[120armv7-quarterly-job-02] `-- Extracting suitesparse-5.2.0_2: .......... done
[120armv7-quarterly-job-02] 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
===>   py27-macs2-2.1.0.p20170505_2 depends on package: py27-numpy>0 - found
===>   Returning to build of py27-macs2-2.1.0.p20170505_2
===>   py27-macs2-2.1.0.p20170505_2 depends on executable: cython-2.7 - not found
===>   Installing existing package /packages/All/py27-cython-0.29.txz
[120armv7-quarterly-job-02] Installing py27-cython-0.29...
[120armv7-quarterly-job-02] Extracting py27-cython-0.29: .......... done
===>   py27-macs2-2.1.0.p20170505_2 depends on executable: cython-2.7 - found
===>   Returning to build of py27-macs2-2.1.0.p20170505_2
===>   py27-macs2-2.1.0.p20170505_2 depends on package: py27-setuptools>0 - found
===>   py27-macs2-2.1.0.p20170505_2 depends on file: /usr/local/bin/python2.7 - found
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for py27-macs2-2.1.0.p20170505_2
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "setup_w_cython.py", line 117, in <module>
    main()
  File "setup_w_cython.py", line 64, in main
    Extension("MACS2.hashtable", ["MACS2/hashtable.pyx"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args),
NameError: global name 'numpy_get_include' is not defined
*** Error code 1

Stop.
make: stopped in /usr/ports/biology/py-macs2



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