Date: Thu, 23 Jan 2014 20:31:20 GMT From: pkg-fallout@FreeBSD.org To: theraven@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [LEGACY - 91amd64-default][biology/biococoa] Build failed for biococoa-2.2.2 during run-depends Message-ID: <201401232031.s0NKVKAC005437@beefy3.isc.freebsd.org>
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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@FreeBSD.org Last committer: theraven@FreeBSD.org Ident: $FreeBSD: head/biology/biococoa/Makefile 329819 2013-10-08 18:34:45Z theraven $ Log URL: http://beefy3.isc.freebsd.org/bulk/91amd64-default/2014-01-23_15h56m33s/logs/biococoa-2.2.2.log Build URL: http://beefy3.isc.freebsd.org/bulk/91amd64-default/2014-01-23_15h56m33s Log: ====>> Building biology/biococoa build started at Thu Jan 23 20:29:28 UTC 2014 port directory: /usr/ports/biology/biococoa building for: FreeBSD pkg.FreeBSD.org 9.1-RELEASE-p10 FreeBSD 9.1-RELEASE-p10 amd64 maintained by: theraven@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 STATUS=1 MASTERMNT=/usr/local/poudriere/data/build/91amd64-default/ref PKG_EXT=tbz FORCE_PACKAGE=yes tpid=16349 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNG=0 PKGNAME=biococoa-2.2.2 PKG_DELETE=pkg_delete PKG_ADD=pkg_add PWD=/root MASTERNAME=91amd64-default USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes PKG_VERSION=pkg_version ---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 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ===> Cleaning for biococoa-2.2.2 =======================<phase: check-config >============================ =========================================================================== =======================<phase: pkg-depends >============================ =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License LGPL21 accepted by the user => biococoa-2.2.2-src.tgz doesn't seem to exist in /distfiles/. => Attempting to fetch http://bioinformatics.org/biococoa/downloads/biococoa-2.2.2-src.tgz biococoa-2.2.2-src.tgz 350 kB 737 kBps ===> 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.tbz ===> 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.tbz makewhatis: /usr/local/lib/perl5/5.16/man: No such file or directory pkg_add: command '/usr/bin/makewhatis /usr/local/lib/perl5/5.16/man' failed 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. ==== 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.tbz 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 ./etc/CORBA missing (created) ./etc/CORBA/servers missing (created) ./etc/X11 missing (created) ./etc/X11/serverconfig missing (created) ./etc/X11/starthere missing (created) ./etc/X11/sysconfig missing (created) ./etc/dconf missing (created) ./etc/dconf/db missing (created) ./etc/dconf/profile missing (created) ./etc/gconf missing (created) ./etc/gconf/gconf.xml.defaults missing (created) ./etc/gconf/gconf.xml.mandatory missing (created) ./etc/gconf/gconf.xml.system missing (created) ./etc/gconf/schemas missing (created) ./etc/gnome missing (created) ./etc/gnome/config missing (created) ./etc/gnome-vfs-2.0 missing (created) ./etc/gnome-vfs-2.0/modules missing (created) ./etc/mateconf missing (created) ./etc/mateconf/mateconf.xml.defaults missing (created) ./etc/mateconf/mateconf.xml.mandatory missing (created) ./etc/mateconf/mateconf.xml.system missing (created) ./etc/mateconf/schemas missing (created) ./etc/sound missing (created) ./etc/sound/events missing (created) ./etc/vfs missing (created) ./etc/vfs/modules missing (created) ./etc/xdg missing (created) ./etc/xdg/autostart missing (created) ./include/gconf missing (created) ./include/gdkcardimage missing (created) ./include/gnome-1.0 missing (created) ./lib/GConf missing (created) ./lib/bonobo missing (created) ./lib/bonobo/monikers missing (created) ./lib/bonobo/plugin missing (created) ./lib/girepository-1.0 missing (created) ./lib/gnome-vfs-2.0 missing (created) ./lib/gnome-vfs-2.0/modules missing (created) ./lib/mate-vfs-2.0 missing (created) ./lib/mate-vfs-2.0/modules missing (created) ./lib/matecomponent missing (created) ./lib/matecomponent/monikers missing (created) ./lib/matecomponent-2.0 missing (created) ./lib/matecomponent-2.0/samples missing (created) ./lib/vfs missing (created) ./lib/vfs/modules missing (created) <snip> 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 ... 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.tbz pkg_add: package 'gnustep-back-0.24.0_1' or its older version already installed *** [run-depends] Error code 1 Stop in /usr/ports/biology/biococoa. ===> Cleaning for biococoa-2.2.2
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