[REL - 10i386-default][biology/biococoa] Failed for biococoa-2.2.2 in run-depends
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Wed Jan 15 15:28:08 UTC 2014
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: theraven at FreeBSD.org
Last committer: theraven at FreeBSD.org
Ident: $FreeBSD: head/biology/biococoa/Makefile 329819 2013-10-08 18:34:45Z theraven $
Log URL: http://beefy1.isc.freebsd.org/bulk/10i386-default/2014-01-15_14h50m10s/logs/biococoa-2.2.2.log
Build URL: http://beefy1.isc.freebsd.org/bulk/10i386-default/2014-01-15_14h50m10s
Log:
====>> Building biology/biococoa
build started at Wed Jan 15 15:27:25 UTC 2014
port directory: /usr/ports/biology/biococoa
building for: FreeBSD 10i386-default-job-22 10.0-RC1 FreeBSD 10.0-RC1 i386
maintained by: theraven at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/biococoa/Makefile 329819 2013-10-08 18:34:45Z theraven $
Poudriere version: 3.1-pre
---Begin Environment---
UNAME_m=i386
UNAME_p=i386
OSVERSION=1000510
UNAME_v=FreeBSD 10.0-RC1
UNAME_r=10.0-RC1
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
MASTERMNT=/usr/local/poudriere/data/build/10i386-default/ref
PKG_EXT=txz
tpid=17107
POUDRIERE_BUILD_TYPE=bulk
PKGNG=1
PKGNAME=biococoa-2.2.2
PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f
PKG_ADD=/usr/local/sbin/pkg-static add
PWD=/root
MASTERNAME=10i386-default
USER=root
HOME=/root
POUDRIERE_VERSION=3.1-pre
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
PKG_VERSION=/poudriere/pkg-static version
PKG_BIN=/usr/local/sbin/pkg-static
---End Environment---
---Begin OPTIONS List---
---End OPTIONS List---
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
TMPDIR="/tmp" MAKE=gmake SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
TMPDIR="/tmp" "CC=/usr/bin/clang CXX=/usr/bin/clang++" SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="/usr/bin/clang" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="/usr/bin/clang-cpp" CPPFLAGS="" LDFLAGS="" CXX="/usr/bin/clang++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing" 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 444" BSD_INSTALL_MAN="install -o root -g wheel -m 444"
--End MAKE_ENV--
--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/biococoa
DOCSDIR=/usr/local/share/doc/biococoa
EXAMPLESDIR=/usr/local/share/examples/biococoa
WWWDIR=/usr/local/www/biococoa
ETCDIR=/usr/local/etc/biococoa
--End SUB_LIST--
---Begin make.conf---
ARCH=i386
MACHINE=i386
MACHINE_ARCH=i386
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
WITH_PKGNG=yes
NO_RESTRICTED=yes
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
===> Cleaning for biococoa-2.2.2
=======================<phase: check-config >============================
===========================================================================
=======================<phase: pkg-depends >============================
===> biococoa-2.2.2 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-1.2.5.txz
Installing pkg-1.2.5... done
If you are upgrading from the old package format, first run:
# pkg2ng
===> Returning to build of biococoa-2.2.2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License LGPL21 accepted by the user
===> Fetching all distfiles required by biococoa-2.2.2 for building
===========================================================================
=======================<phase: checksum >============================
===> License LGPL21 accepted by the user
===> Fetching all distfiles required by biococoa-2.2.2 for building
=> SHA256 Checksum OK for biococoa-2.2.2-src.tgz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License LGPL21 accepted by the user
===> Fetching all distfiles required by biococoa-2.2.2 for building
===> Extracting for biococoa-2.2.2
=> SHA256 Checksum OK for biococoa-2.2.2-src.tgz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for biococoa-2.2.2
===========================================================================
=======================<phase: build-depends >============================
===> biococoa-2.2.2 depends on file: /usr/local/GNUstep/System/Library/Makefiles/GNUstep.sh - not found
===> Verifying install for /usr/local/GNUstep/System/Library/Makefiles/GNUstep.sh in /usr/ports/devel/gnustep-make
===> Installing existing package /packages/All/gnustep-make-2.6.6.txz
Installing gnustep-make-2.6.6...Installing libobjc2-1.7... done
done
===> Returning to build of biococoa-2.2.2
===> biococoa-2.2.2 depends on file: /usr/local/GNUstep/System/Library/Bundles/libgnustep-cairo-023.bundle/libgnustep-cairo-023 - not found
===> Verifying install for /usr/local/GNUstep/System/Library/Bundles/libgnustep-cairo-023.bundle/libgnustep-cairo-023 in /usr/ports/x11-toolkits/gnustep-back
===> Installing existing package /packages/All/gnustep-back-cairo-0.24.0.txz
Installing gnustep-back-cairo-0.24.0...Installing libXrender-0.9.8...Installing kbproto-1.0.6... done
Installing libX11-1.6.2,1...Installing libXau-1.0.8...Installing xproto-7.0.25... done
done
Installing libXdmcp-1.1.1... done
Installing libpthread-stubs-0.3_4... done
Installing libxcb-1.9.3...Installing libxml2-2.8.0_3... done
done
done
Installing renderproto-0.11.1... done
done
Installing libXfixes-5.0.1...Installing fixesproto-5.0... done
done
Installing libXext-1.3.2,1...Installing xextproto-7.2.1... done
done
Installing libXcursor-1.1.14... done
Installing libXt-1.1.4,1...Installing libICE-1.0.8,1... done
Installing libSM-1.2.2,1... done
done
Installing libXmu-1.1.2,1... done
Installing gnustep-gui-0.24.0...Installing libxslt-1.1.28_1...Installing libgpg-error-1.12...Installing gettext-0.18.3.1... done
done
Installing libgcrypt-1.5.3... done
done
Installing aspell-0.60.6.1_3...Installing perl5-5.16.3_6...Removing /usr/local/etc/perl5_version... Done.
Creating /usr/local/etc/perl5_version... Done.
Removing stale symlinks from /usr/bin...
Skipping /usr/bin/perl
Skipping /usr/bin/perl5
Done.
Creating various symlinks in /usr/bin...
Symlinking /usr/local/bin/perl5.16.3 to /usr/bin/perl
Symlinking /usr/local/bin/perl5.16.3 to /usr/bin/perl5
Done.
done
done
Installing gnutls-2.12.23_3...Installing libtasn1-3.3... done
Installing nettle-2.7.1...Installing gmp-5.1.3... done
done
Installing p11-kit-0.20.1...Installing ca_root_nss-3.15.3.1... done
Installing libffi-3.0.13_1... done
done
done
Installing cups-client-1.5.4_1... done
Installing mDNSResponder-541... done
Installing gnustep-base-1.24.6_1...Installing icu-50.1.2... done
done
Installing tiff-4.0.3...Installing freeglut-2.8.1...Installing libGLU-9.0.0...Installing libGL-7.6.1_4...Installing dri2proto-2.8... done
Installing expat-2.1.0... done
Installing libXdamage-1.1.4...Installing damageproto-1.2.1... done
done
Installing libXxf86vm-1.1.3...Installing xf86vidmodeproto-2.3.1... done
done
Installing libdrm-2.4.17_1...Installing libpciaccess-0.13.2...Installing pciids-20131225... done
done
done
done
done
Installing libXi-1.7.2,1...Installing inputproto-2.3... done
done
Installing libXrandr-1.4.2...Installing randrproto-1.4.0... done
done
done
Installing jbigkit-1.6... done
Installing jpeg-8_4... done
done
Installing png-1.5.17... done
Installing giflib-nox11-4.2.3... done
Installing libsndfile-1.0.25_3...Installing libvorbis-1.3.3_1,3...Installing libogg-1.3.1,4... done
done
Installing flac-1.3.0_1... done
done
Installing libao-1.1.0_1... done
Installing flite-1.4... done
done
Installing libXft-2.3.1...Installing fontconfig-2.11.0_1,1...Installing freetype2-2.5.2... done
<snip>
Creating ../../BioCocoa.framework/Versions/2/Headers/BCSequenceStructure.h...
Making build-headers for subproject BCSequence...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCAnnotation.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCSequence.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCSequenceArray.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCSequenceCodon.h...
Making build-headers for subproject BCSequenceIO...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCSequenceReader.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCSequenceWriter.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCCachedSequenceFile.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCCachedFastaFile.h...
Making build-headers for subproject BCSymbol...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCAminoAcid.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCNucleotide.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCSymbol.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCNucleotideDNA.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCNucleotideRNA.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCSymbolSet.h...
Making build-headers for subproject BCTools...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCSequenceTool.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolDigest.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolHydropathyCalculator.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolMassCalculator.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolComplement.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolSequenceFinder.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolSymbolCounter.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolTranslator.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCToolTranslatorDNA.h...
Making build-headers for subproject BCUtils...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCDataMatrix.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCUtilData.h...
Creating ../../BioCocoa.framework/Versions/2/Headers/BCUtilStrings.h...
Making build-headers for subproject BCFoundation...
Creating ../BioCocoa.framework/Versions/2/Headers/BCFoundation.h...
Creating ../BioCocoa.framework/Versions/2/Headers/BCFoundationDefines.h...
Creating ../BioCocoa.framework/Versions/2/Headers/BCStringDefinitions.h...
Creating ../BioCocoa.framework/Versions/2/Headers/BCPreferences.h...
Making build-headers for framework BioCocoa...
Creating derived_src/.stamp...
Creating BioCocoa.framework/Versions/2/Resources...
Updating Version/Current symlink...
Making all in subprojects of framework BioCocoa...
Making all in subprojects of subproject BCFoundation...
Making all for subproject BCAlignment...
Compiling file BCPairwiseAlignment.m ...
Compiling file BCScoreMatrix.m ...
Compiling file BCSequenceAlignment.m ...
Linking subproject BCAlignment ...
clang: warning: argument unused during compilation: '-pthread'
Making all for subproject BCAnalysis...
Compiling file BCMCP.m ...
Compiling file BCSuffixArray.m ...
Linking subproject BCAnalysis ...
clang: warning: argument unused during compilation: '-pthread'
Making all for subproject BCGeneExpression...
Compiling file BCSeries.m ...
Compiling file BCSample.m ...
Compiling file BCPlatform.m ...
Compiling file BCParseSOFT.m ...
Linking subproject BCGeneExpression ...
clang: warning: argument unused during compilation: '-pthread'
Making all for subproject BCGeneticCode...
Compiling file BCCodonDNA.m ...
Compiling file BCCodon.m ...
Compiling file BCCodonRNA.m ...
Compiling file BCGeneticCode.m ...
Linking subproject BCGeneticCode ...
clang: warning: argument unused during compilation: '-pthread'
Making all for subproject BCProteinStructure...
Compiling file BCAtom.m ...
Compiling file BCProteinStructure.m ...
Compiling file BCSecondaryStructure.m ...
Compiling file BCChain.m ...
Compiling file BCResidue.m ...
Compiling file BCSequenceStructure.m ...
Linking subproject BCProteinStructure ...
clang: warning: argument unused during compilation: '-pthread'
Making all for subproject BCSequence...
Compiling file BCAnnotation.m ...
Compiling file BCSequence.m ...
Compiling file BCSequenceArray.m ...
Compiling file BCSequenceCodon.m ...
Linking subproject BCSequence ...
clang: warning: argument unused during compilation: '-pthread'
Making all for subproject BCSequenceIO...
Compiling file BCSequenceReader.m ...
BCSequenceReader.m:167:63: warning: instance method '-initWithRTF:documentAttributes:' not found (return type defaults to 'id') [-Wobjc-method-access]
NSAttributedString *rtfstring = [[NSAttributedString alloc] initWithRTF: [entryString dataUsingEncoding: NSUTF8StringEncoding] documentAttributes: nil];
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BCSequenceReader.m:798:48: warning: incompatible pointer types sending 'id' to parameter of type 'NSString **' [-Wincompatible-pointer-types]
[lineScanner scanUpToString:@" " intoString: nil];
^~~
/usr/local/include/objc/runtime.h:207:14: note: expanded from macro 'nil'
# define nil ((id)_OBJC_NULL_PTR)
^~~~~~~~~~~~~~~~~~~~
/usr/local/GNUstep/System/Library/Headers/Foundation/NSScanner.h:102:68: note: passing argument to parameter 'value' here
- (BOOL) scanUpToString: (NSString*)string intoString: (NSString**)value;
^
BCSequenceReader.m:830:12: warning: using 'stringWithString:' with a literal is redundant [-Wobjc-redundant-literal-use]
name = [NSString stringWithString: @"alignment"];
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3 warnings generated.
Compiling file BCSequenceWriter.m ...
Compiling file BCCachedSequenceFile.m ...
Compiling file BCCachedFastaFile.m ...
BCCachedFastaFile.m:126:71: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
NSLog(@"Attempting to read past end of forward stand: (%lu)\n", aPos);
~~~ ^~~~
%llu
BCCachedFastaFile.m:132:16: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
if (newPos < 0) {
~~~~~~ ^ ~
BCCachedFastaFile.m:133:72: warning: format specifies type 'unsigned long' but the argument has type 'unsigned long long' [-Wformat]
NSLog(@"Attempting to read past end of reverse strand: (%lu)\n", aPos);
~~~ ^~~~
%llu
3 warnings generated.
Linking subproject BCSequenceIO ...
clang: warning: argument unused during compilation: '-pthread'
Making all for subproject BCSymbol...
Compiling file BCAminoAcid.m ...
Compiling file BCNucleotide.m ...
Compiling file BCSymbol.m ...
Compiling file BCNucleotideDNA.m ...
BCNucleotideDNA.m:445:43: warning: 'BCNucleotideDNA' may not respond to 'initWithDictionary:'
aBase = [[[BCNucleotideDNA alloc] initWithDictionary: aBase] autorelease];
~~~~~~~~~~~~~~~~~~~~~~~ ^
1 warning generated.
Compiling file BCNucleotideRNA.m ...
BCNucleotideRNA.m:454:43: warning: 'BCNucleotideRNA' may not respond to 'initWithDictionary:'
aBase = [[[BCNucleotideRNA alloc] initWithDictionary: aBase] autorelease];
~~~~~~~~~~~~~~~~~~~~~~~ ^
1 warning generated.
Compiling file BCSymbolSet.m ...
Linking subproject BCSymbol ...
clang: warning: argument unused during compilation: '-pthread'
Making all for subproject BCTools...
Compiling file BCSequenceTool.m ...
Compiling file BCToolDigest.m ...
Compiling file BCToolHydropathyCalculator.m ...
Compiling file BCToolMassCalculator.m ...
Compiling file BCToolComplement.m ...
Compiling file BCToolSequenceFinder.m ...
Compiling file BCToolSymbolCounter.m ...
Compiling file BCToolTranslator.m ...
Compiling file BCToolTranslatorDNA.m ...
Linking subproject BCTools ...
clang: warning: argument unused during compilation: '-pthread'
Making all for subproject BCUtils...
Compiling file BCDataMatrix.m ...
Compiling file BCUtilData.m ...
Compiling file BCUtilStrings.m ...
BCUtilStrings.m:98:23: warning: incompatible pointer types sending 'id' to parameter of type 'int *' [-Wincompatible-pointer-types]
if ([scanner scanInt:nil])
^~~
/usr/local/include/objc/runtime.h:207:14: note: expanded from macro 'nil'
# define nil ((id)_OBJC_NULL_PTR)
^~~~~~~~~~~~~~~~~~~~
/usr/local/GNUstep/System/Library/Headers/Foundation/NSScanner.h:94:25: note: passing argument to parameter 'value' here
- (BOOL) scanInt: (int*)value;
^
BCUtilStrings.m:100:24: warning: incompatible pointer types sending 'id' to parameter of type 'int *' [-Wincompatible-pointer-types]
if ([scanner scanInt:nil])
^~~
/usr/local/include/objc/runtime.h:207:14: note: expanded from macro 'nil'
# define nil ((id)_OBJC_NULL_PTR)
^~~~~~~~~~~~~~~~~~~~
/usr/local/GNUstep/System/Library/Headers/Foundation/NSScanner.h:94:25: note: passing argument to parameter 'value' here
- (BOOL) scanInt: (int*)value;
^
2 warnings generated.
Linking subproject BCUtils ...
clang: warning: argument unused during compilation: '-pthread'
Making all for subproject BCFoundation...
Compiling file BCStringDefinitions.m ...
Compiling file BCPreferences.m ...
Linking subproject BCFoundation ...
clang: warning: argument unused during compilation: '-pthread'
Making all for framework BioCocoa...
Creating derived_src/NSFramework_BioCocoa.m...
Compiling file derived_src/NSFramework_BioCocoa.m ...
Linking framework BioCocoa ...
Copying resources into the framework wrapper...
Copying resources from subprojects into the framework wrapper...
Creating BioCocoa.framework/Versions/2/Resources/Info-gnustep.plist...
gmake[1]: Leaving directory `/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2'
===========================================================================
=======================<phase: run-depends >============================
===> biococoa-2.2.2 depends on file: /usr/local/GNUstep/System/Library/Makefiles/GNUstep.sh - found
===> biococoa-2.2.2 depends on file: /usr/local/GNUstep/System/Library/Bundles/libgnustep-cairo-023.bundle/libgnustep-cairo-023 - not found
===> Verifying install for /usr/local/GNUstep/System/Library/Bundles/libgnustep-cairo-023.bundle/libgnustep-cairo-023 in /usr/ports/x11-toolkits/gnustep-back
===> Installing existing package /packages/All/gnustep-back-cairo-0.24.0.txz
Installing gnustep-back-cairo-0.24.0...gnustep-back-cairo-0.24.0 already installed
Failed to install the following 1 package(s): /packages/All/gnustep-back-cairo-0.24.0.txz
*** Error code 70
Stop.
make: stopped in /usr/ports/biology/biococoa
===> Cleaning for biococoa-2.2.2
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