[package - head-powerpc64-default][biology/py-biopython] Failed for py27-biopython-1.77 in configure

pkg-fallout at FreeBSD.org pkg-fallout at FreeBSD.org
Thu Jun 11 05:49:30 UTC 2020


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:     mauricio at arareko.net
Last committer: jwb at FreeBSD.org
Ident:          $FreeBSD: head/biology/py-biopython/Makefile 536875 2020-05-29 02:03:29Z jwb $
Log URL:        http://pylon.nyi.freebsd.org/data/head-powerpc64-default/p538068_s361855/logs/py27-biopython-1.77.log
Build URL:      http://pylon.nyi.freebsd.org/build.html?mastername=head-powerpc64-default&build=p538068_s361855
Log:

=>> Building biology/py-biopython
build started at Thu Jun 11 05:48:26 UTC 2020
port directory: /usr/ports/biology/py-biopython
package name: py27-biopython-1.77
building for: FreeBSD head-powerpc64-default-job-02 13.0-CURRENT FreeBSD 13.0-CURRENT 1300097 powerpc
maintained by: mauricio at arareko.net
Makefile ident:      $FreeBSD: head/biology/py-biopython/Makefile 536875 2020-05-29 02:03:29Z jwb $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300084
Jail OSVERSION: 1300097
Job Id: 02




!!! Jail is newer than host. (Jail: 1300097, Host: 1300084) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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

---Begin OPTIONS List---
===> The following configuration options are available for py27-biopython-1.77:
     REPORTLAB=on: PDF support in Bio.Graphics module
===> Use 'make config' to modify these settings
---End OPTIONS List---

--MAINTAINER--
mauricio at arareko.net
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27  HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-biopython/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-biopython/work-py27  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27  HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-biopython/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="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local  LOCALBASE=/usr/local  CC="cc" CFLAGS="-O2 -pipe  -fstack-protector-strong -fno-strict-aliasing "  CPP="cpp" CPPFLAGS=""  LDFLAGS=" -fstack-protector-strong " LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -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/biopython DOCSDIR=/usr/local/share/doc/biopython EXAMPLESDIR=/usr/local/share/examples/biopython  WWWDIR=/usr/local/www/biopython ETCDIR=/usr/local/etc/biopython
--End SUB_LIST--

---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
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CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
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=======================<phase: check-sanity   >============================
===>   NOTICE:

This port is deprecated; you may wish to reconsider installing it:

Uses Python 2.7 which is EOLed upstream.

It is scheduled to be removed on or after 2020-12-31.

===>  License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   py27-biopython-1.77 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.14.4.txz
[head-powerpc64-default-job-02] Installing pkg-1.14.4...
[head-powerpc64-default-job-02] Extracting pkg-1.14.4: .......... done
===>   py27-biopython-1.77 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of py27-biopython-1.77
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>   NOTICE:

This port is deprecated; you may wish to reconsider installing it:

Uses Python 2.7 which is EOLed upstream.

It is scheduled to be removed on or after 2020-12-31.

===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py27-biopython-1.77 for building
===========================================================================
=======================<phase: checksum       >============================
===>   NOTICE:

This port is deprecated; you may wish to reconsider installing it:

Uses Python 2.7 which is EOLed upstream.

It is scheduled to be removed on or after 2020-12-31.

===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py27-biopython-1.77 for building
=> SHA256 Checksum OK for biopython-1.77.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>   NOTICE:

This port is deprecated; you may wish to reconsider installing it:

Uses Python 2.7 which is EOLed upstream.

It is scheduled to be removed on or after 2020-12-31.

===>  License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by py27-biopython-1.77 for building
===>  Extracting for py27-biopython-1.77
=> SHA256 Checksum OK for biopython-1.77.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for py27-biopython-1.77
===========================================================================
=======================<phase: build-depends  >============================
===>   py27-biopython-1.77 depends on package: py27-numpy>=1.16,1<1.19,1 - not found
===>   Installing existing package /packages/All/py27-numpy-1.16.6,1.txz
[head-powerpc64-default-job-02] Installing py27-numpy-1.16.6,1...
[head-powerpc64-default-job-02] `-- Installing gcc9-9.3.0_1...
[head-powerpc64-default-job-02] |   `-- Installing binutils-2.33.1_2,1...
[head-powerpc64-default-job-02] |   | `-- Installing gettext-runtime-0.20.2...
[head-powerpc64-default-job-02] |   |   `-- Installing indexinfo-0.3.1...
[head-powerpc64-default-job-02] |   |   `-- Extracting indexinfo-0.3.1: .... done
[head-powerpc64-default-job-02] |   | `-- Extracting gettext-runtime-0.20.2: .......... done
[head-powerpc64-default-job-02] |   `-- Extracting binutils-2.33.1_2,1: .......... done
[head-powerpc64-default-job-02] |   `-- Installing gmp-6.2.0...
[head-powerpc64-default-job-02] |   `-- Extracting gmp-6.2.0: .......... done
[head-powerpc64-default-job-02] |   `-- Installing mpc-1.1.0_2...
[head-powerpc64-default-job-02] |   | `-- Installing mpfr-4.0.2...
[head-powerpc64-default-job-02] |   | `-- Extracting mpfr-4.0.2: .......... done
[head-powerpc64-default-job-02] |   `-- Extracting mpc-1.1.0_2: ......... done
[head-powerpc64-default-job-02] `-- Extracting gcc9-9.3.0_1: .......... done
[head-powerpc64-default-job-02] `-- Installing openblas-0.3.9_2,1...
[head-powerpc64-default-job-02] `-- Extracting openblas-0.3.9_2,1: .......... done
[head-powerpc64-default-job-02] `-- Installing py27-setuptools-44.0.0...
[head-powerpc64-default-job-02] |   `-- Installing python27-2.7.18...
[head-powerpc64-default-job-02] |   | `-- Installing libffi-3.2.1_3...
[head-powerpc64-default-job-02] |   | `-- Extracting libffi-3.2.1_3: .......... done
[head-powerpc64-default-job-02] |   | `-- Installing readline-8.0.4...
[head-powerpc64-default-job-02] |   | `-- Extracting readline-8.0.4: .......... done
[head-powerpc64-default-job-02] |   `-- Extracting python27-2.7.18: .......... done
[head-powerpc64-default-job-02] `-- Extracting py27-setuptools-44.0.0: .......... done
[head-powerpc64-default-job-02] `-- Installing suitesparse-5.7.2_1...
[head-powerpc64-default-job-02] |   `-- Installing metis-5.1.0_8...
[head-powerpc64-default-job-02] |   `-- Extracting metis-5.1.0_8: .......... done
[head-powerpc64-default-job-02] |   `-- Installing tbb-2020.2...
[head-powerpc64-default-job-02] |   `-- Extracting tbb-2020.2: .......... done
[head-powerpc64-default-job-02] `-- Extracting suitesparse-5.7.2_1: .......... done
[head-powerpc64-default-job-02] Extracting py27-numpy-1.16.6,1: .......... done
=====
Message from gcc9-9.3.0_1:

--
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/gcc9

For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
=====
Message from python27-2.7.18:

--
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
--
===>   NOTICE:

This port is deprecated; you may wish to reconsider installing it:

EOLed upstream.

It is scheduled to be removed on or after 2020-12-31.
=====
Message from py27-setuptools-44.0.0:

--
Only /usr/local/bin/easy_install-2.7 script has been installed
  since Python 2.7 is not the default Python version.
--
===>   NOTICE:

This port is deprecated; you may wish to reconsider installing it:

Uses Python 2.7 which is EOLed upstream.

It is scheduled to be removed on or after 2020-12-31.
=====
Message from py27-numpy-1.16.6,1:

--
===>   NOTICE:

This port is deprecated; you may wish to reconsider installing it:

Uses Python 2.7 which is EOLed upstream.

It is scheduled to be removed on or after 2020-12-31.
===>   py27-biopython-1.77 depends on package: py27-numpy>=1.16,1<1.19,1 - found
===>   Returning to build of py27-biopython-1.77
===>   py27-biopython-1.77 depends on package: py27-setuptools>0 - found
===>   py27-biopython-1.77 depends on file: /usr/local/bin/python2.7 - found
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for py27-biopython-1.77
Biopython requires Python 3.6 or later. Python 2.7 detected.
*** Error code 1

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


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