From owner-freebsd-pkg-fallout@FreeBSD.ORG Wed Jan 22 15:01:05 2014 Return-Path: Delivered-To: pkg-fallout@FreeBSD.org Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 5D6D8E3; Wed, 22 Jan 2014 15:01:05 +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 4728B1163; Wed, 22 Jan 2014 15:01:05 +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 s0MF15Pw041541; Wed, 22 Jan 2014 15:01:05 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy2.isc.freebsd.org (8.14.7/8.14.7/Submit) id s0MF15Fl041501; Wed, 22 Jan 2014 15:01:05 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Wed, 22 Jan 2014 15:01:05 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201401221501.s0MF15Fl041501@beefy2.isc.freebsd.org> To: theraven@FreeBSD.org Subject: [REL - 91amd64-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, 22 Jan 2014 15:01:05 -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/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@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 =================================================== =========================================================================== =================================================== ===> 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_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 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... =========================================================================== =================================================== ===> 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