From owner-freebsd-pkg-fallout@FreeBSD.ORG Wed Jan 15 23:31:52 2014 Return-Path: Delivered-To: pkg-fallout@FreeBSD.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 870ACA7D; Wed, 15 Jan 2014 23:31:52 +0000 (UTC) Received: from beefy2.isc.freebsd.org (beefy2.isc.freebsd.org [IPv6:2001:4f8:3:ffe0:4072:0:16:39]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by mx1.freebsd.org (Postfix) with ESMTPS id 700DB12B3; Wed, 15 Jan 2014 23:31:52 +0000 (UTC) Received: from beefy2.isc.freebsd.org (localhost [127.0.0.1]) by beefy2.isc.freebsd.org (8.14.7/8.14.7) with ESMTP id s0FNVqGQ075601; Wed, 15 Jan 2014 23:31:52 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy2.isc.freebsd.org (8.14.7/8.14.7/Submit) id s0FNVqbT075569; Wed, 15 Jan 2014 23:31:52 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Wed, 15 Jan 2014 23:31:52 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201401152331.s0FNVqbT075569@beefy2.isc.freebsd.org> To: theraven@FreeBSD.org Subject: [REL - head-amd64-default][biology/biococoa] Failed for biococoa-2.2.2 in run-depends Cc: pkg-fallout@FreeBSD.org X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.17 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 15 Jan 2014 23:31:52 -0000 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://beefy2.isc.freebsd.org/bulk/head-amd64-default/2014-01-15_19h51m13s/logs/biococoa-2.2.2.log Build URL: http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2014-01-15_19h51m13s Log: ====>> Building biology/biococoa build started at Wed Jan 15 23:31:01 UTC 2014 port directory: /usr/ports/biology/biococoa building for: FreeBSD head-amd64-default-job-01 11.0-CURRENT FreeBSD 11.0-CURRENT r256430 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=1100000 UNAME_v=FreeBSD 11.0-CURRENT r256430 UNAME_r=11.0-CURRENT 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/head-amd64-default/ref PKG_EXT=txz tpid=37757 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=head-amd64-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--- 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 =================================================== =========================================================================== =================================================== ===> 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 =========================================================================== =================================================== =========================================================================== =================================================== ===> License LGPL21 accepted by the user ===> Fetching all distfiles required by biococoa-2.2.2 for building =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for biococoa-2.2.2 =========================================================================== =================================================== ===> 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 libX11-1.6.2,1...Installing kbproto-1.0.6... done Installing libXau-1.0.8...Installing xproto-7.0.25... done done Installing libXdmcp-1.1.1... done Installing libxcb-1.9.3...Installing libpthread-stubs-0.3_4... done 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 libSM-1.2.2,1...Installing libICE-1.0.8,1... done 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-9.1.7...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-2.4.50...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 flac-1.3.0_1...Installing libogg-1.3.1,4... done done Installing libvorbis-1.3.3_1,3... 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 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 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... gmake[1]: Leaving directory `/wrkdirs/usr/ports/biology/biococoa/work/biococoa-2.2.2' =========================================================================== =================================================== ===> 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