[REL - 91amd64-default][biology/biococoa] Failed for biococoa-2.2.2 in run-depends
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Wed Jan 22 15:01:05 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://beefy2.isc.freebsd.org/bulk/91amd64-default/2014-01-22_12h05m01s/logs/biococoa-2.2.2.log
Build URL: http://beefy2.isc.freebsd.org/bulk/91amd64-default/2014-01-22_12h05m01s
Log:
====>> Building biology/biococoa
build started at Wed Jan 22 14:59:19 UTC 2014
port directory: /usr/ports/biology/biococoa
building for: FreeBSD 91amd64-default-job-05 9.1-RELEASE-p10 FreeBSD 9.1-RELEASE-p10 amd64
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---
OSVERSION=901000
UNAME_v=FreeBSD 9.1-RELEASE-p10
UNAME_r=9.1-RELEASE-p10
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/91amd64-default/ref
PKG_EXT=txz
tpid=88527
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=91amd64-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/local/bin/clang33 CXX=/usr/local/bin/clang++33" SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="/usr/local/bin/clang33" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="/usr/local/bin/clang-cpp33" CPPFLAGS="" LDFLAGS="" CXX="/usr/local/bin/clang++33" 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---
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_1... done
done
===> Returning to build of biococoa-2.2.2
===> biococoa-2.2.2 depends on file: /usr/local/bin/clang33 - not found
===> Verifying install for /usr/local/bin/clang33 in /usr/ports/lang/clang33
===> Installing existing package /packages/All/clang33-3.3_4.txz
Installing clang33-3.3_4...Installing llvm33-3.3_7...Installing libexecinfo-1.1_3... done
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
Installing python27-2.7.6_1...Installing gettext-0.18.3.1...Installing libiconv-1.14_1... done
done
done
done
done
====
Note that some of the standard modules are provided as separate
ports since they require extra dependencies:
bsddb databases/py-bsddb
gdbm databases/py-gdbm
sqlite3 databases/py-sqlite3
tkinter x11-toolkits/py-tkinter
Install them as needed.
====
===> Returning to build of biococoa-2.2.2
===> biococoa-2.2.2 depends on file: /usr/local/GNUstep/System/Library/Bundles/libgnustep-cairo-024.bundle/libgnustep-cairo-024 - not found
===> Verifying install for /usr/local/GNUstep/System/Library/Bundles/libgnustep-cairo-024.bundle/libgnustep-cairo-024 in /usr/ports/x11-toolkits/gnustep-back
===> Installing existing package /packages/All/gnustep-back-0.24.0_1.txz
Installing gnustep-back-0.24.0_1...Installing cairo-1.10.2_7,2...Installing xcb-util-renderutil-0.3.8...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
Installing xcb-util-0.3.9_1,1... done
done
Installing pixman-0.32.4... done
Installing libXrender-0.9.8...Installing kbproto-1.0.6... done
Installing libX11-1.6.2,1... done
Installing renderproto-0.11.1... done
done
Installing fontconfig-2.11.0_1,1...Installing expat-2.1.0... done
Installing freetype2-2.5.2... done
Running fc-cache to build fontconfig cache...
/usr/local/share/fonts: skipping, no such directory
/usr/local/lib/X11/fonts: caching, new cache contents: 0 fonts, 1 dirs
/usr/local/lib/X11/fonts/local: caching, new cache contents: 0 fonts, 0 dirs
/root/.local/share/fonts: skipping, no such directory
/root/.fonts: skipping, no such directory
/usr/local/share/fonts: skipping, no such directory
/usr/local/lib/X11/fonts: caching, new cache contents: 0 fonts, 1 dirs
/root/.local/share/fonts: skipping, no such directory
/root/.fonts: skipping, no such directory
/var/db/fontconfig: cleaning cache directory
/root/.cache/fontconfig: not cleaning non-existent cache directory
/root/.fontconfig: not cleaning non-existent cache directory
fc-cache: succeeded
done
Installing png-1.5.17... done
Installing pcre-8.33... done
Installing libffi-3.0.13_1... done
Installing glib-2.36.3_1...No schema files found: doing nothing.
done
done
Installing giflib-nox11-4.2.3... done
Installing gnustep-gui-0.24.0...Installing libXt-1.1.4,1...Installing libICE-1.0.8,1... done
Installing libSM-1.2.2,1... done
done
Installing libxslt-1.1.28_1...Installing libgpg-error-1.12... done
Installing libgcrypt-1.5.3... done
done
Installing aspell-0.60.6.1_3... 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
<snip>
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 ...
BCParseSOFT.m:259:61: warning: format specifies type 'int' but the argument has type 'NSUInteger' (aka 'unsigned long') [-Wformat]
NSLog(@"ERROR: probe set columns %d != %d entries\n", [probeSetColumns count], [f count]);
~~ ^~~~~~~~~~~~~~~~~~~~~~~
%lu
BCParseSOFT.m:259:86: warning: format specifies type 'int' but the argument has type 'NSUInteger' (aka 'unsigned long') [-Wformat]
NSLog(@"ERROR: probe set columns %d != %d entries\n", [probeSetColumns count], [f count]);
~~ ^~~~~~~~~
%lu
BCParseSOFT.m:332:63: warning: format specifies type 'int' but the argument has type 'NSUInteger' (aka 'unsigned long') [-Wformat]
NSLog(@"ERROR: sample data columns %d != %d entries\n", [sampleSetColumns count], [f count]);
~~ ^~~~~~~~~~~~~~~~~~~~~~~~
%lu
BCParseSOFT.m:332:89: warning: format specifies type 'int' but the argument has type 'NSUInteger' (aka 'unsigned long') [-Wformat]
NSLog(@"ERROR: sample data columns %d != %d entries\n", [sampleSetColumns count], [f count]);
~~ ^~~~~~~~~
%lu
4 warnings generated.
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 ...
BCDataMatrix.m:261:93: warning: format specifies type 'int' but the argument has type 'NSUInteger' (aka 'unsigned long') [-Wformat]
NSLog(@"Invalid matrix format for data matrix, expected %d items, got %d", expectCols, [a count]);
~~ ^~~~~~~~~
%lu
BCDataMatrix.m:341:77: warning: format specifies type 'int' but the argument has type 'NSUInteger' (aka 'unsigned long') [-Wformat]
NSLog(@"Invalid list format for data matrix, expected 3 items, got %d", [a count]);
~~ ^~~~~~~~~
%lu
2 warnings generated.
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...
===========================================================================
=======================<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-024.bundle/libgnustep-cairo-024 - not found
===> Verifying install for /usr/local/GNUstep/System/Library/Bundles/libgnustep-cairo-024.bundle/libgnustep-cairo-024 in /usr/ports/x11-toolkits/gnustep-back
===> Installing existing package /packages/All/gnustep-back-0.24.0_1.txz
Installing gnustep-back-0.24.0_1...gnustep-back-0.24.0_1 already installed
Failed to install the following 1 package(s): /packages/All/gnustep-back-0.24.0_1.txz
*** [run-depends] Error code 70
Stop in /usr/ports/biology/biococoa.
===> Cleaning for biococoa-2.2.2
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