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Date:      Tue, 16 Apr 2019 14:29:32 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 120armv7-quarterly][biology/unanimity] Failed for unanimity-3.4.1 in configure
Message-ID:  <201904161429.x3GETWhi015912@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: jwb@FreeBSD.org
Ident:          $FreeBSD: branches/2019Q2/biology/unanimity/Makefile 493769 2019-02-24 16:04:58Z jwb $
Log URL:        http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/499069/logs/unanimity-3.4.1.log
Build URL:      http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=499069
Log:

=>> Building biology/unanimity
build started at Tue Apr 16 14:28:35 UTC 2019
port directory: /usr/ports/biology/unanimity
package name: unanimity-3.4.1
building for: FreeBSD 120armv7-quarterly-job-16 12.0-RELEASE-p3 FreeBSD 12.0-RELEASE-p3 1200086 arm
maintained by: jwb@FreeBSD.org
Makefile ident:      $FreeBSD: branches/2019Q2/biology/unanimity/Makefile 493769 2019-02-24 16:04:58Z jwb $
Poudriere version: 3.2.8-3-g02cc9753
Host OSVERSION: 1300009
Jail OSVERSION: 1200086
Job Id: 16

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---End OPTIONS List---

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

--CONFIGURE_ARGS--
--prefix /usr/local  --mandir man  --infodir share/info --buildtype release  --strip  _build
--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/unanimity/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/unanimity/work  HOME=/wrkdirs/usr/ports/biology/unanimity/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/unanimity/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/unanimity/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/unanimity/work  HOME=/wrkdirs/usr/ports/biology/unanimity/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/unanimity/work/.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 DESTDIR=/wrkdirs/usr/ports/biology/unanimity/work/stage LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local  LOCALBASE=/usr/local  CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe  -isystem /usr/local/include -fno-strict-aliasing "  CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="-isystem /usr/local/include"  LDFLAGS=" -lexecinfo " LIBS="-L/usr/local/lib"  CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include "  MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install  -s -m 555"  BSD_INSTALL_LIB="install  -s -m 0644"  BSD_INSTALL_SCRIPT="install  -m 555"  BSD_INST
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--End PLIST_SUB--

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

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#### /usr/ports/Mk/Scripts/ports_env.sh ####
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=======================<phase: check-sanity   >============================
===>  License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   unanimity-3.4.1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.5_5.txz
[120armv7-quarterly-job-16] Installing pkg-1.10.5_5...
[120armv7-quarterly-job-16] Extracting pkg-1.10.5_5: .......... done
===>   unanimity-3.4.1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of unanimity-3.4.1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License BSD3CLAUSE accepted by the user
=> PacificBiosciences-unanimity-v3.4.1_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/PacificBiosciences/unanimity/tar.gz/v3.4.1?dummy=/PacificBiosciences-unanimity-v3.4.1_GH0.tar.gz
fetch: https://codeload.github.com/PacificBiosciences/unanimity/tar.gz/v3.4.1?dummy=/PacificBiosciences-unanimity-v3.4.1_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/PacificBiosciences/unanimity/tar.gz/v3.4.1?dummy=/PacificBiosciences-unanimity-v3.4.1_GH0.tar.gz: size of remote file is not known
PacificBiosciences-unanimity-v3.4.1_GH0.tar.gz        6341 kB 9053 kBps    00s
===> Fetching all distfiles required by unanimity-3.4.1 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by unanimity-3.4.1 for building
<snip>
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 python27-2.7.16:

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

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
===>   unanimity-3.4.1 depends on package: py27-numpy>0 - found
===>   Returning to build of unanimity-3.4.1
===>   unanimity-3.4.1 depends on executable: meson - not found
===>   Installing existing package /packages/All/meson-0.49.2.txz
[120armv7-quarterly-job-16] Installing meson-0.49.2...
[120armv7-quarterly-job-16] `-- Installing ninja-1.8.2_1,2...
[120armv7-quarterly-job-16] `-- Extracting ninja-1.8.2_1,2: ......... done
[120armv7-quarterly-job-16] `-- Installing py36-setuptools-40.8.0...
[120armv7-quarterly-job-16] |   `-- Installing python36-3.6.8_1...
[120armv7-quarterly-job-16] |   `-- Extracting python36-3.6.8_1: .......... done
[120armv7-quarterly-job-16] `-- Extracting py36-setuptools-40.8.0: .......... done
[120armv7-quarterly-job-16] Extracting meson-0.49.2: .......... done
Message from python36-3.6.8_1:

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

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

===========================================================================
Message from py36-setuptools-40.8.0:

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

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

*******************************************************************
===>   unanimity-3.4.1 depends on executable: meson - found
===>   Returning to build of unanimity-3.4.1
===>   unanimity-3.4.1 depends on executable: ninja - found
===>   unanimity-3.4.1 depends on package: pkgconf>=1.3.0_1 - not found
===>   Installing existing package /packages/All/pkgconf-1.6.0,1.txz
[120armv7-quarterly-job-16] Installing pkgconf-1.6.0,1...
[120armv7-quarterly-job-16] Extracting pkgconf-1.6.0,1: .......... done
===>   unanimity-3.4.1 depends on package: pkgconf>=1.3.0_1 - found
===>   Returning to build of unanimity-3.4.1
===>   unanimity-3.4.1 depends on file: /usr/local/bin/python2.7 - found
===========================================================================
=======================<phase: lib-depends    >============================
===>   unanimity-3.4.1 depends on shared library: libhts.so - not found
===>   Installing existing package /packages/All/htslib-1.9.txz
[120armv7-quarterly-job-16] Installing htslib-1.9...
[120armv7-quarterly-job-16] `-- Installing curl-7.64.1_1...
[120armv7-quarterly-job-16] |   `-- Installing ca_root_nss-3.43...
[120armv7-quarterly-job-16] |   `-- Extracting ca_root_nss-3.43: ........ done
[120armv7-quarterly-job-16] |   `-- Installing libnghttp2-1.37.0...
[120armv7-quarterly-job-16] |   `-- Extracting libnghttp2-1.37.0: .......... done
[120armv7-quarterly-job-16] `-- Extracting curl-7.64.1_1: .......... done
[120armv7-quarterly-job-16] Extracting htslib-1.9: .......... done
Message from ca_root_nss-3.43:

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

***************************************************************************
===>   unanimity-3.4.1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===>   Returning to build of unanimity-3.4.1
===>   unanimity-3.4.1 depends on shared library: libboost_regex.so - not found
===>   Installing existing package /packages/All/boost-libs-1.69.0_2.txz
[120armv7-quarterly-job-16] Installing boost-libs-1.69.0_2...
[120armv7-quarterly-job-16] `-- Installing icu-64.1,1...
[120armv7-quarterly-job-16] `-- Extracting icu-64.1,1: .......... done
[120armv7-quarterly-job-16] Extracting boost-libs-1.69.0_2: .......... done
Message from boost-libs-1.69.0_2:

You have built the Boost library with thread support.

Don't forget to add -pthread to your linker options when
linking your code.
===>   unanimity-3.4.1 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so)
===>   Returning to build of unanimity-3.4.1
===>   unanimity-3.4.1 depends on shared library: libpbbam.so.0.18.0 - not found
===>   Installing existing package /packages/All/pbbam-0.18.0.txz
[120armv7-quarterly-job-16] Installing pbbam-0.18.0...
[120armv7-quarterly-job-16] Extracting pbbam-0.18.0: .......... done
===>   unanimity-3.4.1 depends on shared library: libpbbam.so.0.18.0 - found (/usr/local/lib/libpbbam.so.0.18.0)
===>   Returning to build of unanimity-3.4.1
===>   unanimity-3.4.1 depends on shared library: libpbcopper.so.0.4.1 - not found
===>   Installing existing package /packages/All/pbcopper-0.4.1.txz
[120armv7-quarterly-job-16] Installing pbcopper-0.4.1...
[120armv7-quarterly-job-16] Extracting pbcopper-0.4.1: .......... done
===>   unanimity-3.4.1 depends on shared library: libpbcopper.so.0.4.1 - found (/usr/local/lib/libpbcopper.so.0.4.1)
===>   Returning to build of unanimity-3.4.1
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for unanimity-3.4.1
The Meson build system
Version: 0.49.2
Source dir: /wrkdirs/usr/ports/biology/unanimity/work/unanimity-3.4.1
Build dir: /wrkdirs/usr/ports/biology/unanimity/work/unanimity-3.4.1/_build
Build type: native build
Project name: UNANIMITY
Project version: 3.0.0
Appending CFLAGS from environment: '-O2 -pipe  -isystem /usr/local/include -fno-strict-aliasing '
Appending LDFLAGS from environment: ' -lexecinfo '
Appending CPPFLAGS from environment: '-isystem /usr/local/include'
Native C compiler: /nxb-bin/usr/bin/cc (clang 6.0.1 "FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1)")
Appending CXXFLAGS from environment: '-O2 -pipe -isystem /usr/local/include -fno-strict-aliasing  -isystem /usr/local/include '
Appending LDFLAGS from environment: ' -lexecinfo '
Appending CPPFLAGS from environment: '-isystem /usr/local/include'
Native C++ compiler: /nxb-bin/usr/bin/c++ (clang 6.0.1 "FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1)")
Build machine cpu family: arm
Build machine cpu: arm
Compiler for C++ supports arguments -Wno-unused-parameter: YES
Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES
Compiler for C++ supports arguments -Wno-unused-variable: YES
Compiler for C++ supports arguments -Wno-sign-compare: YES
Compiler for C++ supports arguments -Wno-unused-local-typedef: YES
Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor: YES
Compiler for C++ supports arguments -Wno-dynamic-class-memaccess: YES
Dependency threads found: YES 
Dependency Boost found: YES 1.69
Found pkg-config: /usr/local/bin/pkgconf (1.6.0)
Dependency pbbam found: YES 0.18.0
Dependency pbcopper found: YES 0.4.1
Dependency zlib found: YES 1.2.10
Dependency seqan-2 found: YES 2.4.0
Configuring UnanimityVersion.cpp using configuration
Configuring ModelInternalInitializer.cpp using configuration
Program python2.7 found: YES (/usr/local/bin/python2.7)
Program swig3.0 found: YES (/usr/local/bin/swig3.0)
Message: Python version: 2.7
Configuring python_sitedir.py using configuration
Message: Python modules will be installed into: /usr/local/lib/python2.7/site-packages
Dependency python-2.7 found: YES 2.7

swig/meson.build:4:2: ERROR:  Problem encountered: Could not determine NumPy includedir!

A full log can be found at /wrkdirs/usr/ports/biology/unanimity/work/unanimity-3.4.1/_build/meson-logs/meson-log.txt
===>  Script "configure" failed unexpectedly.
Please report the problem to jwb@FreeBSD.org [maintainer] and attach the
"/wrkdirs/usr/ports/biology/unanimity/work/unanimity-3.4.1/_build/meson-logs/meson-log.txt"
including the output of the failure of your make command. Also, it might be
a good idea to provide an overview of all packages installed on your system
(e.g. a /usr/local/sbin/pkg-static info -g -Ea).
*** Error code 1

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



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