[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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PORT_FLAGS=
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FLAVOR=py27
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--
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PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/biopython" EXAMPLESDIR="share/examples/biopython" DATADIR="share/biopython" WWWDIR="www/biopython" ETCDIR="etc/biopython"
--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
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
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CC_OUTPUT_921dbbb2_f0b4d593=yes
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CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
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PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
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virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
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kqueues (-k) unlimited
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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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