[package - 101i386-default][biology/ncbi-blast+] Failed for ncbi-blast+-2.2.30_2 in configure
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Mon Apr 27 02:38:02 UTC 2015
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: jwbacon at tds.net
Last committer: marino at FreeBSD.org
Ident: $FreeBSD: head/biology/ncbi-blast+/Makefile 384733 2015-04-25 14:21:58Z marino $
Log URL: http://beefy5.nyi.freebsd.org/data/101i386-default/384800/logs/ncbi-blast+-2.2.30_2.log
Build URL: http://beefy5.nyi.freebsd.org/build.html?mastername=101i386-default&build=384800
Log:
====>> Building biology/ncbi-blast+
build started at Mon Apr 27 02:37:39 UTC 2015
port directory: /usr/ports/biology/ncbi-blast+
building for: FreeBSD 101i386-default-job-16 10.1-RELEASE-p9 FreeBSD 10.1-RELEASE-p9 i386
maintained by: jwbacon at tds.net
Makefile ident: $FreeBSD: head/biology/ncbi-blast+/Makefile 384733 2015-04-25 14:21:58Z marino $
Poudriere version: 3.1.4
Host OSVERSION: 1100064
Jail OSVERSION: 1001000
---Begin Environment---
UNAME_p=i386
UNAME_m=i386
OSVERSION=1001000
UNAME_v=FreeBSD 10.1-RELEASE-p9
UNAME_r=10.1-RELEASE-p9
BLOCKSIZE=K
MAIL=/var/mail/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
STATUS=1
SAVED_TERM=screen
MASTERMNT=/usr/local/poudriere/data/.m/101i386-default/ref
POUDRIERE_BUILD_TYPE=bulk
PKGNAME=ncbi-blast+-2.2.30_2
OLDPWD=/
PWD=/usr/local/poudriere/data/.m/101i386-default/ref/.p/pool
MASTERNAME=101i386-default
SCRIPTPREFIX=/usr/local/share/poudriere
USER=root
HOME=/root
POUDRIERE_VERSION=3.1.4
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
LIBEXECPREFIX=/usr/local/libexec/poudriere
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
---End Environment---
---Begin OPTIONS List---
---End OPTIONS List---
--CONFIGURE_ARGS--
AR="ar cr" --without-boost --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
ncbi_cv_prog_amq_w=no MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work TMPDIR="/tmp" NO_PIE=yes SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="gcc48" CFLAGS="-O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing" CPP="cpp48" CPPFLAGS="" LDFLAGS=" -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48" LIBS="" CXX="g++48" CXXFLAGS="-O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/
usr/local/lib/gcc48" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 0644" BSD_INSTALL_MAN="install -o root -g wheel -m 444"
--End MAKE_ENV--
--PLIST_SUB--
PYTHON_INCLUDEDIR=include/python2.7
PYTHON_LIBDIR=lib/python2.7
PYTHON_PLATFORM=freebsd10
PYTHON_SITELIBDIR=lib/python2.7/site-packages
PYTHON_VERSION=python2.7
PYTHON_VER=2.7
OSREL=10.1
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
PERL_VERSION=5.18.4
PERL_VER=5.18
PERL5_MAN3=lib/perl5/site_perl/man/man3
SITE_PERL=lib/perl5/site_perl
SITE_ARCH=lib/perl5/site_perl/mach/5.18
DOCSDIR="share/doc/blast+"
EXAMPLESDIR="share/examples/blast+"
DATADIR="share/blast+"
WWWDIR="www/blast+"
ETCDIR="etc/blast+"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/blast+
DOCSDIR=/usr/local/share/doc/blast+
EXAMPLESDIR=/usr/local/share/examples/blast+
WWWDIR=/usr/local/www/blast+
ETCDIR=/usr/local/etc/blast+
--End SUB_LIST--
---Begin make.conf---
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
MASTER_SITE_FREEBSD=yes
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
=======================<phase: check-sanity >============================
===> License Public_domain accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> ncbi-blast+-2.2.30_2 depends on file: /usr/local/sbin/pkg - not found
===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg
===> Installing existing package /packages/All/pkg-1.5.1.txz
[101i386-default-job-16] Installing pkg-1.5.1...
[101i386-default-job-16] Extracting pkg-1.5.1... done
Message for pkg-1.5.1:
If you are upgrading from the old package format, first run:
# pkg2ng
===> Returning to build of ncbi-blast+-2.2.30_2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License Public_domain accepted by the user
===> Fetching all distfiles required by ncbi-blast+-2.2.30_2 for building
===========================================================================
=======================<phase: checksum >============================
===> License Public_domain accepted by the user
===> Fetching all distfiles required by ncbi-blast+-2.2.30_2 for building
=> SHA256 Checksum OK for ncbi-blast-2.2.30+-src.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License Public_domain accepted by the user
===> Fetching all distfiles required by ncbi-blast+-2.2.30_2 for building
===> Extracting for ncbi-blast+-2.2.30_2
=> SHA256 Checksum OK for ncbi-blast-2.2.30+-src.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for ncbi-blast+-2.2.30_2
/usr/bin/sed -i.bak -e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|' -e '/--infodir=DIR/d' -e '/--mandir=DIR/d' /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/build-system/configure
/usr/bin/sed -i.bak -e 's|@prefix@|/wrkdirs/usr/ports/biology/ncbi-blast+/work/stage at prefix@|g' /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/build-system/Makefile.in.top
===========================================================================
=======================<phase: build-depends >============================
===> ncbi-blast+-2.2.30_2 depends on executable: gmake - not found
===> Verifying install for gmake in /usr/ports/devel/gmake
===> Installing existing package /packages/All/gmake-4.1_1.txz
[101i386-default-job-16] Installing gmake-4.1_1...
[101i386-default-job-16] `-- Installing gettext-runtime-0.19.4...
[101i386-default-job-16] | `-- Installing indexinfo-0.2.3...
[101i386-default-job-16] | `-- Extracting indexinfo-0.2.3... done
[101i386-default-job-16] `-- Extracting gettext-runtime-0.19.4... done
[101i386-default-job-16] Extracting gmake-4.1_1... done
===> Returning to build of ncbi-blast+-2.2.30_2
===> ncbi-blast+-2.2.30_2 depends on file: /usr/local/bin/python2.7 - not found
===> Verifying install for /usr/local/bin/python2.7 in /usr/ports/lang/python27
===> Installing existing package /packages/All/python27-2.7.9_1.txz
[101i386-default-job-16] Installing python27-2.7.9_1...
[101i386-default-job-16] `-- Installing libffi-3.2.1...
[101i386-default-job-16] `-- Extracting libffi-3.2.1... done
[101i386-default-job-16] Extracting python27-2.7.9_1... done
Message for python27-2.7.9_1:
=====================================================================
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
=====================================================================
===> Returning to build of ncbi-blast+-2.2.30_2
===> ncbi-blast+-2.2.30_2 depends on executable: gcc48 - not found
===> Verifying install for gcc48 in /usr/ports/lang/gcc
===> Installing existing package /packages/All/gcc-4.8.4_1.txz
[101i386-default-job-16] Installing gcc-4.8.4_1...
[101i386-default-job-16] `-- Installing binutils-2.25...
[101i386-default-job-16] `-- Extracting binutils-2.25... done
[101i386-default-job-16] `-- Installing gcc-ecj-4.5...
[101i386-default-job-16] `-- Extracting gcc-ecj-4.5... done
[101i386-default-job-16] `-- Installing gmp-5.1.3_2...
[101i386-default-job-16] `-- Extracting gmp-5.1.3_2... done
[101i386-default-job-16] `-- Installing mpc-1.0.3...
[101i386-default-job-16] | `-- Installing mpfr-3.1.2_2...
[101i386-default-job-16] | `-- Extracting mpfr-3.1.2_2... done
[101i386-default-job-16] `-- Extracting mpc-1.0.3... done
[101i386-default-job-16] Extracting gcc-4.8.4_1... done
Message for gcc-4.8.4_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/gcc48
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> Returning to build of ncbi-blast+-2.2.30_2
===> ncbi-blast+-2.2.30_2 depends on file: /usr/local/bin/as - found
===> ncbi-blast+-2.2.30_2 depends on file: /usr/local/bin/perl5.18.4 - not found
===> Verifying install for /usr/local/bin/perl5.18.4 in /usr/ports/lang/perl5.18
===> Installing existing package /packages/All/perl5-5.18.4_13.txz
[101i386-default-job-16] Installing perl5-5.18.4_13...
[101i386-default-job-16] Extracting perl5-5.18.4_13... done
===> Returning to build of ncbi-blast+-2.2.30_2
===========================================================================
=======================<phase: lib-depends >============================
===> ncbi-blast+-2.2.30_2 depends on shared library: libpcre.so - not found
===> Verifying for libpcre.so in /usr/ports/devel/pcre
===> Installing existing package /packages/All/pcre-8.35_2.txz
[101i386-default-job-16] Installing pcre-8.35_2...
[101i386-default-job-16] Extracting pcre-8.35_2... done
===> Returning to build of ncbi-blast+-2.2.30_2
===> ncbi-blast+-2.2.30_2 depends on shared library: libbz2.so - found (/usr/lib/libbz2.so)
===========================================================================
=======================<phase: configure >============================
===> Configuring for ncbi-blast+-2.2.30_2
configure: error: --localstatedir=/var: unknown option; use --help to show usage
===> Script "configure" failed unexpectedly.
Please report the problem to jwbacon at tds.net [maintainer] and attach the
"/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/config.log"
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/ncbi-blast+
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