[package - head-armv6-default][biology/py-biopython] Failed for py27-biopython-1.70 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sat Sep 9 22:33:53 UTC 2017
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: wen at FreeBSD.org
Ident: $FreeBSD: head/biology/py-biopython/Makefile 448228 2017-08-18 12:57:06Z wen $
Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p449469_s323330/logs/py27-biopython-1.70.log
Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p449469_s323330
Log:
====>> Building biology/py-biopython
build started at Sat Sep 9 22:32:52 UTC 2017
port directory: /usr/ports/biology/py-biopython
building for: FreeBSD head-armv6-default-job-23 12.0-CURRENT FreeBSD 12.0-CURRENT 1200043 arm
maintained by: mauricio at arareko.net
Makefile ident: $FreeBSD: head/biology/py-biopython/Makefile 448228 2017-08-18 12:57:06Z wen $
Poudriere version: 3.1.19-63-g681eaae7
Host OSVERSION: 1200040
Jail OSVERSION: 1200043
Job Id: 23
!!! Jail is newer than host. (Jail: 1200043, Host: 1200040) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/csh
UNAME_p=armv6
UNAME_m=arm
ABI_FILE=/usr/lib/crt1.o
OSVERSION=1200043
UNAME_v=FreeBSD 12.0-CURRENT 1200043
UNAME_r=12.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref
QEMU_EMULATING=1
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
PKGNAME=py27-biopython-1.70
OLDPWD=/
PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool
MASTERNAME=head-armv6-default
SCRIPTPREFIX=/usr/local/share/poudriere
USER=root
HOME=/root
POUDRIERE_VERSION=3.1.19-63-g681eaae7
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
LIBEXECPREFIX=/usr/local/libexec/poudriere
LOCALBASE=/usr/local
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for py27-biopython-1.70:
REPORTLAB=on: PDF support in Bio.Graphics module
===> Use 'make config' to modify these settings
---End OPTIONS List---
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-biopython/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biopython/work HOME=/wrkdirs/usr/ports/biology/py-biopython/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-biopython/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biopython/work HOME=/wrkdirs/usr/ports/biology/py-biopython/work TMPDIR="/tmp" 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 LIBDIR="/usr/lib" 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--
PYTHON_INCLUDEDIR=include/python2.7
PYTHON_LIBDIR=lib/python2.7
PYTHON_PLATFORM=freebsd12
PYTHON_PYOEXTENSION=pyo
PYTHON_SITELIBDIR=lib/python2.7/site-packages
PYTHON_SUFFIX=27
PYTHON_VER=2.7
PYTHON_VERSION=python2.7
PYTHON2=""
PYTHON3="@comment
"
OSREL=12.0
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
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---
.sinclude "/etc/make.nxb.conf"
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
MACHINE=arm
MACHINE_ARCH=armv6
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
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
ARCH=armv6
CONFIGURE_MAX_CMD_LEN=262144
OPSYS=FreeBSD
OSREL=12.0
OSVERSION=1200043
PYTHONBASE=/usr/local
UID=0
_JAVA_OS_LIST_REGEXP=native|linux
_JAVA_VENDOR_LIST_REGEXP=openjdk|oracle|sun
_JAVA_VERSION_LIST_REGEXP=1.6|1.7|1.8|1.6\+|1.7\+|1.8\+
_OSRELEASE=12.0-CURRENT
#### Misc Poudriere ####
GID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
---Begin make.nxb.conf---
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
---End make.nxb.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
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 >============================
===========================================================================
=======================<phase: pkg-depends >============================
===> py27-biopython-1.70 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.10.1.txz
[head-armv6-default-job-23] Installing pkg-1.10.1...
[head-armv6-default-job-23] Extracting pkg-1.10.1: .......... done
===> py27-biopython-1.70 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py27-biopython-1.70
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> Fetching all distfiles required by py27-biopython-1.70 for building
===========================================================================
=======================<phase: checksum >============================
===> Fetching all distfiles required by py27-biopython-1.70 for building
=> SHA256 Checksum OK for biopython-1.70.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> Fetching all distfiles required by py27-biopython-1.70 for building
===> Extracting for py27-biopython-1.70
=> SHA256 Checksum OK for biopython-1.70.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for py27-biopython-1.70
===========================================================================
=======================<phase: build-depends >============================
===> py27-biopython-1.70 depends on file: /usr/local/lib/python2.7/site-packages/numpy/core/numeric.py - not found
===> Installing existing package /packages/All/py27-numpy-1.13.1_1,1.txz
[head-armv6-default-job-23] Installing py27-numpy-1.13.1_1,1...
[head-armv6-default-job-23] `-- Installing blas-3.5.0_3...
[head-armv6-default-job-23] | `-- Installing gcc5-5.4.0_3...
[head-armv6-default-job-23] | | `-- Installing binutils-2.28,1...
[head-armv6-default-job-23] | | `-- Installing gettext-runtime-0.19.8.1_1...
[head-armv6-default-job-23] | | | `-- Installing indexinfo-0.2.6...
[head-armv6-default-job-23] | | | `-- Extracting indexinfo-0.2.6: .... done
[head-armv6-default-job-23] | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done
[head-armv6-default-job-23] | | `-- Extracting binutils-2.28,1: .......... done
[head-armv6-default-job-23] | | `-- Installing gmp-6.1.2...
[head-armv6-default-job-23] | | `-- Extracting gmp-6.1.2: .......... done
[head-armv6-default-job-23] | | `-- Installing mpc-1.0.3...
[head-armv6-default-job-23] | | `-- Installing mpfr-3.1.5_1...
[head-armv6-default-job-23] | | `-- Extracting mpfr-3.1.5_1: .......... done
[head-armv6-default-job-23] | | `-- Extracting mpc-1.0.3: ...... done
[head-armv6-default-job-23] | `-- Extracting gcc5-5.4.0_3: .......... done
[head-armv6-default-job-23] `-- Extracting blas-3.5.0_3: ....... done
[head-armv6-default-job-23] `-- Installing cblas-1.0_6...
[head-armv6-default-job-23] `-- Extracting cblas-1.0_6: ......... done
[head-armv6-default-job-23] `-- Installing lapack-3.5.0_2...
[head-armv6-default-job-23] `-- Extracting lapack-3.5.0_2: .......... done
[head-armv6-default-job-23] `-- Installing py27-setuptools-36.2.2...
[head-armv6-default-job-23] | `-- Installing python27-2.7.13_7...
[head-armv6-default-job-23] | | `-- Installing libffi-3.2.1_1...
[head-armv6-default-job-23] | | `-- Extracting libffi-3.2.1_1: .......... done
[head-armv6-default-job-23] | | `-- Installing readline-7.0.3...
[head-armv6-default-job-23] | | `-- Extracting readline-7.0.3: .......... done
[head-armv6-default-job-23] | `-- Extracting python27-2.7.13_7: .......... done
[head-armv6-default-job-23] `-- Extracting py27-setuptools-36.2.2: .......... done
[head-armv6-default-job-23] `-- Installing suitesparse-4.0.2_6...
[head-armv6-default-job-23] | `-- Installing openblas-0.2.20,1...
[head-armv6-default-job-23] | `-- Extracting openblas-0.2.20,1: ......... done
[head-armv6-default-job-23] `-- Extracting suitesparse-4.0.2_6: .......... done
[head-armv6-default-job-23] Extracting py27-numpy-1.13.1_1,1: .......... done
Message from gcc5-5.4.0_3:
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/gcc5
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
Message from cblas-1.0_6:
===> 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 python27-2.7.13_7:
===========================================================================
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
===========================================================================
===> py27-biopython-1.70 depends on file: /usr/local/lib/python2.7/site-packages/numpy/core/numeric.py - found
===> Returning to build of py27-biopython-1.70
===> py27-biopython-1.70 depends on package: py27-setuptools>0 - found
===> py27-biopython-1.70 depends on file: /usr/local/bin/python2.7 - found
===> py27-biopython-1.70 depends on executable: python2 - not found
===> Installing existing package /packages/All/python2-2_3.txz
[head-armv6-default-job-23] Installing python2-2_3...
[head-armv6-default-job-23] Extracting python2-2_3: ...... done
===> py27-biopython-1.70 depends on executable: python2 - found
===> Returning to build of py27-biopython-1.70
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for py27-biopython-1.70
running config
===========================================================================
=======================<phase: build >============================
===> Building for py27-biopython-1.70
running build
running build_py
Missing required dependency NumPy (Numerical Python).
Unless running under Jython or IronPython, we require NumPy be installed
when compiling Biopython. See http://www.numpy.org for details.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/py-biopython
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