Date: Sat, 29 Oct 2016 21:27:42 GMT From: pkg-fallout@FreeBSD.org To: wenheping@gmail.com Cc: pkg-fallout@FreeBSD.org Subject: [package - head-i386-default][biology/biojava] Failed for biojava-1.7, 1 in extract Message-ID: <201610292127.u9TLRgDY027526@beefy3.nyi.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: wenheping@gmail.com Last committer: mat@FreeBSD.org Ident: $FreeBSD: head/biology/biojava/Makefile 418767 2016-07-19 11:04:13Z mat $ Log URL: http://beefy3.nyi.freebsd.org/data/head-i386-default/p424740_s307979/logs/biojava-1.7,1.log Build URL: http://beefy3.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p424740_s307979 Log: ====>> Building biology/biojava build started at Sat Oct 29 21:27:37 UTC 2016 port directory: /usr/ports/biology/biojava building for: FreeBSD head-i386-default-job-14 12.0-CURRENT FreeBSD 12.0-CURRENT r307979 i386 maintained by: wenheping@gmail.com Makefile ident: $FreeBSD: head/biology/biojava/Makefile 418767 2016-07-19 11:04:13Z mat $ Poudriere version: 3.1.14 Host OSVERSION: 1200005 Jail OSVERSION: 1200014 !!! Jail is newer than host. (Jail: 1200014, Host: 1200005) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 UNAME_v=FreeBSD 12.0-CURRENT r307979 UNAME_r=12.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=i386 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/head-i386-default/ref UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ POUDRIERE_BUILD_TYPE=bulk PKGNAME=biojava-1.7,1 OSREL=12.0 _OSRELEASE=12.0-CURRENT PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=24 PWD=/usr/local/poudriere/data/.m/head-i386-default/ref/.p/pool MASTERNAME=head-i386-default SCRIPTPREFIX=/usr/local/share/poudriere _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun USER=root HOME=/root POUDRIERE_VERSION=3.1.14 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh CONFIGURE_MAX_CMD_LEN=262144 LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes _JAVA_OS_LIST_REGEXP=native\|linux OSVERSION=1200014 ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for biojava-1.7,1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/biojava/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/biojava/work HOME=/wrkdirs/usr/ports/biology/biojava/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- CLASSPATH="/usr/local/share/java/classes" JAVA_HOME=/usr/local/openjdk8 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/biojava/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/biojava/work HOME=/wrkdirs/usr/ports/biology/biojava/work TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/biojava" EXAMPLESDIR="share/examples/biojava" DATADIR="share/biojava" WWWDIR="www/biojava" ETCDIR="etc/biojava" --End PLIST_SUB-- --SUB_LIST-- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="1.6+" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/biojava DOCSDIR=/usr/local/share/doc/biojava EXAMPLESDIR=/usr/local/share/examples/biojava WWWDIR=/usr/local/www/biojava ETCDIR=/usr/local/etc/biojava --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- =======================<phase: check-sanity >============================ =========================================================================== =======================<phase: pkg-depends >============================ ===> biojava-1.7,1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.9.1.txz [head-i386-default-job-14] Installing pkg-1.9.1... [head-i386-default-job-14] Extracting pkg-1.9.1: .......... done ===> biojava-1.7,1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of biojava-1.7,1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> Fetching all distfiles required by biojava-1.7,1 for building =========================================================================== =======================<phase: checksum >============================ ===> Fetching all distfiles required by biojava-1.7,1 for building => SHA256 Checksum OK for biojava-1.7-all.jar. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> Fetching all distfiles required by biojava-1.7,1 for building ===> Extracting for biojava-1.7,1 => SHA256 Checksum OK for biojava-1.7-all.jar. META-INF/MANIFEST.MF: Could not stat META-INF/MANIFEST.MF biojava-1.7/apps/: Could not stat biojava-1.7/apps biojava-1.7/apps/org/: Could not stat biojava-1.7/apps/org biojava-1.7/apps/org/biojava/: Could not stat biojava-1.7/apps/org/biojava biojava-1.7/apps/org/biojava/app/: Could not stat biojava-1.7/apps/org/biojava/app biojava-1.7/apps/org/biojava/app/BioFlatIndex.java: Could not stat biojava-1.7/apps/org/biojava/app/BioFlatIndex.java biojava-1.7/apps/org/biojava/app/BioGetSeq.java: Could not stat biojava-1.7/apps/org/biojava/app/BioGetSeq.java biojava-1.7/apps-1.7.jar: Could not stat biojava-1.7/apps-1.7.jar biojava-1.7/biojava-1.7.jar: Could not stat biojava-1.7/biojava-1.7.jar biojava-1.7/build.xml: Could not stat biojava-1.7/build.xml biojava-1.7/bytecode.jar: Could not stat biojava-1.7/bytecode.jar biojava-1.7/commons-cli.jar: Could not stat biojava-1.7/commons-cli.jar biojava-1.7/commons-collections-2.1.jar: Could not stat biojava-1.7/commons-collections-2.1.jar biojava-1.7/commons-dbcp-1.1.jar: Could not stat biojava-1.7/commons-dbcp-1.1.jar biojava-1.7/commons-pool-1.1.jar: Could not stat biojava-1.7/commons-pool-1.1.jar biojava-1.7/demos/: Could not stat biojava-1.7/demos biojava-1.7/demos/annodb/: Could not stat biojava-1.7/demos/annodb biojava-1.7/demos/annodb/CreateIndexDB.java: Could not stat biojava-1.7/demos/annodb/CreateIndexDB.java biojava-1.7/demos/biosql/: Could not stat biojava-1.7/demos/biosql biojava-1.7/demos/biosql/DummyFromGFF.java: Could not stat biojava-1.7/demos/biosql/DummyFromGFF.java biojava-1.7/demos/biosql/LargeSequenceTest.java: Could not stat biojava-1.7/demos/biosql/LargeSequenceTest.java biojava-1.7/demos/biosql/SeqDumper.java: Could not stat biojava-1.7/demos/biosql/SeqDumper.java biojava-1.7/demos/biosql/SeqEMBL.java: Could not stat biojava-1.7/demos/biosql/SeqEMBL.java biojava-1.7/demos/biosql/SeqGFF.java: Could not stat biojava-1.7/demos/biosql/SeqGFF.java biojava-1.7/demos/biosql/SequenceTest.java: Could not stat biojava-1.7/demos/biosql/SequenceTest.java biojava-1.7/demos/biosql/UploadFlat.java: Could not stat biojava-1.7/demos/biosql/UploadFlat.java biojava-1.7/demos/blastxml/: Could not stat biojava-1.7/demos/blastxml biojava-1.7/demos/blastxml/BlastParser.java: Could not stat biojava-1.7/demos/blastxml/BlastParser.java biojava-1.7/demos/blastxml/input.xml: Could not stat biojava-1.7/demos/blastxml/input.xml biojava-1.7/demos/CircLocTest/: Could not stat biojava-1.7/demos/CircLocTest biojava-1.7/demos/CircLocTest/CircularLocationTester.java: Could not stat biojava-1.7/demos/CircLocTest/CircularLocationTester.java biojava-1.7/demos/CircLocTest/TestFrame.java: Could not stat biojava-1.7/demos/CircLocTest/TestFrame.java biojava-1.7/demos/das/: Could not stat biojava-1.7/demos/das biojava-1.7/demos/das/TestDAS.java: Could not stat biojava-1.7/demos/das/TestDAS.java biojava-1.7/demos/das/TestDASG.java: Could not stat biojava-1.7/demos/das/TestDASG.java biojava-1.7/demos/das/TestDASH.java: Could not stat biojava-1.7/demos/das/TestDASH.java biojava-1.7/demos/das/TestDSN.java: Could not stat biojava-1.7/demos/das/TestDSN.java biojava-1.7/demos/dist/: Could not stat biojava-1.7/demos/dist biojava-1.7/demos/dist/TestDistribution.java: Could not stat biojava-1.7/demos/dist/TestDistribution.java biojava-1.7/demos/dist/TestOrderNAlphabet.java: Could not stat biojava-1.7/demos/dist/TestOrderNAlphabet.java biojava-1.7/demos/dist/TestOrderNDistribution.java: Could not stat biojava-1.7/demos/dist/TestOrderNDistribution.java biojava-1.7/demos/dist/Tools.java: Could not stat biojava-1.7/demos/dist/Tools.java biojava-1.7/demos/dp/: Could not stat biojava-1.7/demos/dp biojava-1.7/demos/dp/Dice.java: Could not stat biojava-1.7/demos/dp/Dice.java biojava-1.7/demos/dp/fake.fasta: Could not stat biojava-1.7/demos/dp/fake.fasta biojava-1.7/demos/dp/fakepromoter.xml: Could not stat biojava-1.7/demos/dp/fakepromoter.xml biojava-1.7/demos/dp/package.html: Could not stat biojava-1.7/demos/dp/package.html <snip> biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBIblastn2_0_11Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBIblastn2_0_11Test.java biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBIblastn2_2_3Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBIblastn2_2_3Test.java biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBIblastp2_0_11Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBIblastp2_0_11Test.java biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBIblastp2_2_3Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBIblastp2_2_3Test.java biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBIblastx2_0_11Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBIblastx2_0_11Test.java biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBIblastx2_2_3Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBIblastx2_2_3Test.java biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBItblastn2_0_11Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBItblastn2_0_11Test.java biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBItblastn2_2_3Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBItblastn2_2_3Test.java biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBItblastx2_0_11Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBItblastx2_0_11Test.java biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBItblastx2_2_3Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindNCBItblastx2_2_3Test.java biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindWUblastn2_0a19Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindWUblastn2_0a19Test.java biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindWUblastp2_0a19Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindWUblastp2_0a19Test.java biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindWUblastx2_0a19Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindWUblastx2_0a19Test.java biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindWUtblastn2_0a19Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindWUtblastn2_0a19Test.java biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindWUtblastx2_0a19Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/program/ssbind/SSBindWUtblastx2_0a19Test.java biojava-1.7/tests/org/biojava/bio/proteomics/: Could not stat biojava-1.7/tests/org/biojava/bio/proteomics biojava-1.7/tests/org/biojava/bio/proteomics/aaindex/: Could not stat biojava-1.7/tests/org/biojava/bio/proteomics/aaindex biojava-1.7/tests/org/biojava/bio/proteomics/aaindex/AAindexStreamReaderTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/proteomics/aaindex/AAindexStreamReaderTest.java biojava-1.7/tests/org/biojava/bio/proteomics/aaindex/AAindexTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/proteomics/aaindex/AAindexTest.java biojava-1.7/tests/org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDBTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/proteomics/aaindex/SimpleSymbolPropertyTableDBTest.java biojava-1.7/tests/org/biojava/bio/proteomics/IsoelectricPointCalcTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/proteomics/IsoelectricPointCalcTest.java biojava-1.7/tests/org/biojava/bio/proteomics/MassCalcTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/proteomics/MassCalcTest.java biojava-1.7/tests/org/biojava/bio/search/: Could not stat biojava-1.7/tests/org/biojava/bio/search biojava-1.7/tests/org/biojava/bio/search/MaxMismatchPatternTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/search/MaxMismatchPatternTest.java biojava-1.7/tests/org/biojava/bio/search/SeqContentPatternTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/search/SeqContentPatternTest.java biojava-1.7/tests/org/biojava/bio/search/SimpleSeqSimilaritySearchHitTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/search/SimpleSeqSimilaritySearchHitTest.java biojava-1.7/tests/org/biojava/bio/search/SimpleSeqSimilaritySearchResultTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/search/SimpleSeqSimilaritySearchResultTest.java biojava-1.7/tests/org/biojava/bio/search/SimpleSeqSimilaritySearchSubHitTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/search/SimpleSeqSimilaritySearchSubHitTest.java biojava-1.7/tests/org/biojava/bio/seq/: Could not stat biojava-1.7/tests/org/biojava/bio/seq biojava-1.7/tests/org/biojava/bio/seq/CircularSequenceTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/CircularSequenceTest.java biojava-1.7/tests/org/biojava/bio/seq/db/: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db biojava-1.7/tests/org/biojava/bio/seq/db/AbstractSequenceDBTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/AbstractSequenceDBTest.java biojava-1.7/tests/org/biojava/bio/seq/db/biosql/: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/biosql biojava-1.7/tests/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/biosql/BioSQLSequenceDBTest.java biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/emblcd biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/acnum.hit: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/acnum.hit biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/acnum.trg: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/acnum.trg biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/division.lkp: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/division.lkp biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/DivisionLkpReaderTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/DivisionLkpReaderTest.java biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/entrynam.idx: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/entrynam.idx biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/EntryNamIdxReaderTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/EntryNamIdxReaderTest.java biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/EntryNamRandomAccessTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/EntryNamRandomAccessTest.java biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/protDB1.aa: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/protDB1.aa biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/protDB2.aa: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/protDB2.aa biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/protDB3.aa: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/emblcd/protDB3.aa biojava-1.7/tests/org/biojava/bio/seq/db/EmblCDROMIndexStoreTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/EmblCDROMIndexStoreTest.java biojava-1.7/tests/org/biojava/bio/seq/db/HashSequenceDBTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/HashSequenceDBTest.java biojava-1.7/tests/org/biojava/bio/seq/db/TestHashSequenceDB.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/db/TestHashSequenceDB.java biojava-1.7/tests/org/biojava/bio/seq/DNAToolsTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/DNAToolsTest.java biojava-1.7/tests/org/biojava/bio/seq/FeatureFilterTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/FeatureFilterTest.java biojava-1.7/tests/org/biojava/bio/seq/FeatureHolderUtilsTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/FeatureHolderUtilsTest.java biojava-1.7/tests/org/biojava/bio/seq/filter/: Could not stat biojava-1.7/tests/org/biojava/bio/seq/filter biojava-1.7/tests/org/biojava/bio/seq/filter/FilterTransformerTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/filter/FilterTransformerTest.java biojava-1.7/tests/org/biojava/bio/seq/FilterUtilsTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/FilterUtilsTest.java biojava-1.7/tests/org/biojava/bio/seq/homol/: Could not stat biojava-1.7/tests/org/biojava/bio/seq/homol biojava-1.7/tests/org/biojava/bio/seq/homol/SimpleSimilarityPairFeatureTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/homol/SimpleSimilarityPairFeatureTest.java biojava-1.7/tests/org/biojava/bio/seq/impl/: Could not stat biojava-1.7/tests/org/biojava/bio/seq/impl biojava-1.7/tests/org/biojava/bio/seq/impl/GappedSequenceTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/impl/GappedSequenceTest.java biojava-1.7/tests/org/biojava/bio/seq/impl/SubSequenceTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/impl/SubSequenceTest.java biojava-1.7/tests/org/biojava/bio/seq/impl/ViewSeqSerializationTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/impl/ViewSeqSerializationTest.java biojava-1.7/tests/org/biojava/bio/seq/impl/ViewSequenceTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/impl/ViewSequenceTest.java biojava-1.7/tests/org/biojava/bio/seq/io/: Could not stat biojava-1.7/tests/org/biojava/bio/seq/io biojava-1.7/tests/org/biojava/bio/seq/io/filterxml/: Could not stat biojava-1.7/tests/org/biojava/bio/seq/io/filterxml biojava-1.7/tests/org/biojava/bio/seq/io/filterxml/FilterXMLTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/io/filterxml/FilterXMLTest.java biojava-1.7/tests/org/biojava/bio/seq/io/LocationFormatterTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/io/LocationFormatterTest.java biojava-1.7/tests/org/biojava/bio/seq/io/MSFAlignmentFormatTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/io/MSFAlignmentFormatTest.java biojava-1.7/tests/org/biojava/bio/seq/io/SeqIOToolsTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/io/SeqIOToolsTest.java biojava-1.7/tests/org/biojava/bio/seq/io/SmartSequenceBuilderTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/io/SmartSequenceBuilderTest.java biojava-1.7/tests/org/biojava/bio/seq/io/SymbolListCharSequenceTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/io/SymbolListCharSequenceTest.java biojava-1.7/tests/org/biojava/bio/seq/MergeFeatureHolderTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/MergeFeatureHolderTest.java biojava-1.7/tests/org/biojava/bio/seq/NewSimpleAssemblyTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/NewSimpleAssemblyTest.java biojava-1.7/tests/org/biojava/bio/seq/project/: Could not stat biojava-1.7/tests/org/biojava/bio/seq/project biojava-1.7/tests/org/biojava/bio/seq/project/ProjectedFeatureHolderTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/project/ProjectedFeatureHolderTest.java biojava-1.7/tests/org/biojava/bio/seq/ProteinToolsTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/ProteinToolsTest.java biojava-1.7/tests/org/biojava/bio/seq/RNAToolsTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/RNAToolsTest.java biojava-1.7/tests/org/biojava/bio/seq/SeqSerializationTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/SeqSerializationTest.java biojava-1.7/tests/org/biojava/bio/seq/SimpleAssemblyTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/seq/SimpleAssemblyTest.java biojava-1.7/tests/org/biojava/bio/structure/: Could not stat biojava-1.7/tests/org/biojava/bio/structure biojava-1.7/tests/org/biojava/bio/structure/MMcifTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/structure/MMcifTest.java biojava-1.7/tests/org/biojava/bio/structure/PdbFileFormat30Test.java: Could not stat biojava-1.7/tests/org/biojava/bio/structure/PdbFileFormat30Test.java biojava-1.7/tests/org/biojava/bio/structure/PDBFileParserTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/structure/PDBFileParserTest.java biojava-1.7/tests/org/biojava/bio/structure/SourceCompoundTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/structure/SourceCompoundTest.java biojava-1.7/tests/org/biojava/bio/structure/StructurePairAlignerTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/structure/StructurePairAlignerTest.java biojava-1.7/tests/org/biojava/bio/structure/StructureTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/structure/StructureTest.java biojava-1.7/tests/org/biojava/bio/structure/StructureToolsTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/structure/StructureToolsTest.java biojava-1.7/tests/org/biojava/bio/symbol/: Could not stat biojava-1.7/tests/org/biojava/bio/symbol biojava-1.7/tests/org/biojava/bio/symbol/AbstractSymbolEventTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/AbstractSymbolEventTest.java biojava-1.7/tests/org/biojava/bio/symbol/AlphabetManagerTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/AlphabetManagerTest.java biojava-1.7/tests/org/biojava/bio/symbol/AlphabetSerializationTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/AlphabetSerializationTest.java biojava-1.7/tests/org/biojava/bio/symbol/BetweenLocationTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/BetweenLocationTest.java biojava-1.7/tests/org/biojava/bio/symbol/CircularLocationTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/CircularLocationTest.java biojava-1.7/tests/org/biojava/bio/symbol/CodonPrefToolsTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/CodonPrefToolsTest.java biojava-1.7/tests/org/biojava/bio/symbol/CompoundLocationTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/CompoundLocationTest.java biojava-1.7/tests/org/biojava/bio/symbol/CrossProductAlphabetIndexTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/CrossProductAlphabetIndexTest.java biojava-1.7/tests/org/biojava/bio/symbol/CrossProductTokenizationTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/CrossProductTokenizationTest.java biojava-1.7/tests/org/biojava/bio/symbol/DoubleAlphabetTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/DoubleAlphabetTest.java biojava-1.7/tests/org/biojava/bio/symbol/FundamentalAtomicSymbolEventTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/FundamentalAtomicSymbolEventTest.java biojava-1.7/tests/org/biojava/bio/symbol/GappedSymbolListTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/GappedSymbolListTest.java biojava-1.7/tests/org/biojava/bio/symbol/IndexedNoAmbPackTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/IndexedNoAmbPackTest.java biojava-1.7/tests/org/biojava/bio/symbol/IntegerAlphabetTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/IntegerAlphabetTest.java biojava-1.7/tests/org/biojava/bio/symbol/LinearAlphabetIndexTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/LinearAlphabetIndexTest.java biojava-1.7/tests/org/biojava/bio/symbol/MergeLocationTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/MergeLocationTest.java biojava-1.7/tests/org/biojava/bio/symbol/MotifToolsTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/MotifToolsTest.java biojava-1.7/tests/org/biojava/bio/symbol/NameTokenizationTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/NameTokenizationTest.java biojava-1.7/tests/org/biojava/bio/symbol/PointLocationTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/PointLocationTest.java biojava-1.7/tests/org/biojava/bio/symbol/RangeLocationTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/RangeLocationTest.java biojava-1.7/tests/org/biojava/bio/symbol/SimpleAtomicSymbolEventTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/SimpleAtomicSymbolEventTest.java biojava-1.7/tests/org/biojava/bio/symbol/SimpleBasisSymbolEventTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/SimpleBasisSymbolEventTest.java biojava-1.7/tests/org/biojava/bio/symbol/SimpleCodonPrefTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/SimpleCodonPrefTest.java biojava-1.7/tests/org/biojava/bio/symbol/SimpleSymbolEventTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/SimpleSymbolEventTest.java biojava-1.7/tests/org/biojava/bio/symbol/SimpleSymbolListTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/SimpleSymbolListTest.java biojava-1.7/tests/org/biojava/bio/symbol/SimpleWobbleDistributionTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/SimpleWobbleDistributionTest.java biojava-1.7/tests/org/biojava/bio/symbol/SymbolListTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/SymbolListTest.java biojava-1.7/tests/org/biojava/bio/symbol/SymbolSerializationTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/SymbolSerializationTest.java biojava-1.7/tests/org/biojava/bio/symbol/SymbolUtils.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/SymbolUtils.java biojava-1.7/tests/org/biojava/bio/symbol/TestSoftMaskedAlphabet.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/TestSoftMaskedAlphabet.java biojava-1.7/tests/org/biojava/bio/symbol/TranslationTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/TranslationTest.java biojava-1.7/tests/org/biojava/bio/symbol/UkkonenSuffixTreeTest.java: Could not stat biojava-1.7/tests/org/biojava/bio/symbol/UkkonenSuffixTreeTest.java biojava-1.7/tests/org/biojava/directory/: Could not stat biojava-1.7/tests/org/biojava/directory biojava-1.7/tests/org/biojava/directory/OBDARegistryParserTest.java: Could not stat biojava-1.7/tests/org/biojava/directory/OBDARegistryParserTest.java biojava-1.7/tests/org/biojava/directory/RegistryConfigurationTest.java: Could not stat biojava-1.7/tests/org/biojava/directory/RegistryConfigurationTest.java biojava-1.7/tests/org/biojava/directory/seqdatabase.ini: Could not stat biojava-1.7/tests/org/biojava/directory/seqdatabase.ini biojava-1.7/tests/org/biojava/directory/SystemRegistryTest.java: Could not stat biojava-1.7/tests/org/biojava/directory/SystemRegistryTest.java biojava-1.7/tests/org/biojava/naming/: Could not stat biojava-1.7/tests/org/biojava/naming biojava-1.7/tests/org/biojava/naming/ObdaInitialContextFactoryTest.java: Could not stat biojava-1.7/tests/org/biojava/naming/ObdaInitialContextFactoryTest.java biojava-1.7/tests/org/biojava/naming/ObdaUriParserTest.java: Could not stat biojava-1.7/tests/org/biojava/naming/ObdaUriParserTest.java biojava-1.7/tests/org/biojava/ontology/: Could not stat biojava-1.7/tests/org/biojava/ontology biojava-1.7/tests/org/biojava/ontology/OntologyTest.java: Could not stat biojava-1.7/tests/org/biojava/ontology/OntologyTest.java biojava-1.7/tests/org/biojava/ontology/ParseOBOFileTest.java: Could not stat biojava-1.7/tests/org/biojava/ontology/ParseOBOFileTest.java biojava-1.7/tests/org/biojava/ontology/TermImplTest.java: Could not stat biojava-1.7/tests/org/biojava/ontology/TermImplTest.java biojava-1.7/tests/org/biojava/ontology/TripleImplTest.java: Could not stat biojava-1.7/tests/org/biojava/ontology/TripleImplTest.java biojava-1.7/tests/org/biojava/utils/: Could not stat biojava-1.7/tests/org/biojava/utils biojava-1.7/tests/org/biojava/utils/automata/: Could not stat biojava-1.7/tests/org/biojava/utils/automata biojava-1.7/tests/org/biojava/utils/automata/NfaTest.java: Could not stat biojava-1.7/tests/org/biojava/utils/automata/NfaTest.java biojava-1.7/tests/org/biojava/utils/ListToolsTest.java: Could not stat biojava-1.7/tests/org/biojava/utils/ListToolsTest.java biojava-1.7/tests/org/biojava/utils/lsid/: Could not stat biojava-1.7/tests/org/biojava/utils/lsid biojava-1.7/tests/org/biojava/utils/lsid/LifeScienceIdentifierTest.java: Could not stat biojava-1.7/tests/org/biojava/utils/lsid/LifeScienceIdentifierTest.java biojava-1.7/tests/org/biojava/utils/process/: Could not stat biojava-1.7/tests/org/biojava/utils/process biojava-1.7/tests/org/biojava/utils/process/AllTests.java: Could not stat biojava-1.7/tests/org/biojava/utils/process/AllTests.java biojava-1.7/tests/org/biojava/utils/process/ExternalProcessTest.java: Could not stat biojava-1.7/tests/org/biojava/utils/process/ExternalProcessTest.java biojava-1.7/tests/org/biojava/utils/regex/: Could not stat biojava-1.7/tests/org/biojava/utils/regex biojava-1.7/tests/org/biojava/utils/regex/PatternCheckerTest.java: Could not stat biojava-1.7/tests/org/biojava/utils/regex/PatternCheckerTest.java biojava-1.7/tests/org/biojava/utils/regex/RegexTest.java: Could not stat biojava-1.7/tests/org/biojava/utils/regex/RegexTest.java biojava-1.7/tests/org/biojava/utils/RepeatedCharSequenceTest.java: Could not stat biojava-1.7/tests/org/biojava/utils/RepeatedCharSequenceTest.java biojava-1.7/tests/org/biojava/utils/SmallMapTest.java: Could not stat biojava-1.7/tests/org/biojava/utils/SmallMapTest.java biojava-1.7/tests/org/biojava/utils/walker/: Could not stat biojava-1.7/tests/org/biojava/utils/walker biojava-1.7/tests/org/biojava/utils/walker/WalkerFactoryTest.java: Could not stat biojava-1.7/tests/org/biojava/utils/walker/WalkerFactoryTest.java biojava-1.7/tests/org/biojava/utils/walker/WalkerTest.java: Could not stat biojava-1.7/tests/org/biojava/utils/walker/WalkerTest.java biojava-1.7/tests/org/biojavax/: Could not stat biojava-1.7/tests/org/biojavax biojava-1.7/tests/org/biojavax/bio/: Could not stat biojava-1.7/tests/org/biojavax/bio biojava-1.7/tests/org/biojavax/bio/seq/: Could not stat biojava-1.7/tests/org/biojavax/bio/seq biojava-1.7/tests/org/biojavax/bio/seq/CompoundRichLocationTest.java: Could not stat biojava-1.7/tests/org/biojavax/bio/seq/CompoundRichLocationTest.java biojava-1.7/tests/org/biojavax/bio/seq/io/: Could not stat biojava-1.7/tests/org/biojavax/bio/seq/io biojava-1.7/tests/org/biojavax/bio/seq/io/Bug2249_2248Test.java: Could not stat biojava-1.7/tests/org/biojavax/bio/seq/io/Bug2249_2248Test.java biojava-1.7/tests/org/biojavax/bio/seq/io/Bug2250_2256Test.java: Could not stat biojava-1.7/tests/org/biojavax/bio/seq/io/Bug2250_2256Test.java biojava-1.7/tests/org/biojavax/bio/seq/io/Bug2255Test.java: Could not stat biojava-1.7/tests/org/biojavax/bio/seq/io/Bug2255Test.java biojava-1.7/tests/org/biojavax/bio/seq/io/EMBLFormatTest.java: Could not stat biojava-1.7/tests/org/biojavax/bio/seq/io/EMBLFormatTest.java biojava-1.7/tests/org/biojavax/bio/seq/io/GenbankFormatTest.java: Could not stat biojava-1.7/tests/org/biojavax/bio/seq/io/GenbankFormatTest.java biojava-1.7/tests/org/biojavax/bio/seq/io/INSDseqFormatTest.java: Could not stat biojava-1.7/tests/org/biojavax/bio/seq/io/INSDseqFormatTest.java biojava-1.7/tests/org/biojavax/bio/seq/io/UniProtFormatTest.java: Could not stat biojava-1.7/tests/org/biojavax/bio/seq/io/UniProtFormatTest.java biojava-1.7/tests/org/biojavax/bio/seq/MultiSourceCompoundRichLocationTest.java: Could not stat biojava-1.7/tests/org/biojavax/bio/seq/MultiSourceCompoundRichLocationTest.java biojava-1.7/tests/org/biojavax/bio/seq/SimpleRichFeatureTest.java: Could not stat biojava-1.7/tests/org/biojavax/bio/seq/SimpleRichFeatureTest.java biojava-1.7/tests/org/biojavax/bio/seq/SimpleRichLocationTest.java: Could not stat biojava-1.7/tests/org/biojavax/bio/seq/SimpleRichLocationTest.java biojava-1.7/tests/org/biojavax/bio/SimpleBioEntryTest.java: Could not stat biojava-1.7/tests/org/biojavax/bio/SimpleBioEntryTest.java biojava-1.7/tests/org/biojavax/bio/taxa/: Could not stat biojava-1.7/tests/org/biojavax/bio/taxa biojava-1.7/tests/org/biojavax/bio/taxa/SimpleNCBITaxonNameTest.java: Could not stat biojava-1.7/tests/org/biojavax/bio/taxa/SimpleNCBITaxonNameTest.java biojava-1.7/tests/org/biojavax/CrossReferenceResolutionExceptionTest.java: Could not stat biojava-1.7/tests/org/biojavax/CrossReferenceResolutionExceptionTest.java biojava-1.7/tests/org/biojavax/DummyCrossReferenceResolverTest.java: Could not stat biojava-1.7/tests/org/biojavax/DummyCrossReferenceResolverTest.java biojava-1.7/tests/org/biojavax/EmptyRichAnnotationTest.java: Could not stat biojava-1.7/tests/org/biojavax/EmptyRichAnnotationTest.java biojava-1.7/tests/org/biojavax/ga/: Could not stat biojava-1.7/tests/org/biojavax/ga biojava-1.7/tests/org/biojavax/ga/functions/: Could not stat biojava-1.7/tests/org/biojavax/ga/functions biojava-1.7/tests/org/biojavax/ga/functions/AbstractCrossOverFunctionTest.java: Could not stat biojava-1.7/tests/org/biojavax/ga/functions/AbstractCrossOverFunctionTest.java biojava-1.7/tests/org/biojavax/ga/functions/AbstractMutationFunctionTest.java: Could not stat biojava-1.7/tests/org/biojavax/ga/functions/AbstractMutationFunctionTest.java biojava-1.7/tests/org/biojavax/ga/functions/ProportionalSelectionTest.java: Could not stat biojava-1.7/tests/org/biojavax/ga/functions/ProportionalSelectionTest.java biojava-1.7/tests/org/biojavax/ga/functions/SimpleCrossOverFunctionTest.java: Could not stat biojava-1.7/tests/org/biojavax/ga/functions/SimpleCrossOverFunctionTest.java biojava-1.7/tests/org/biojavax/ga/functions/SimpleMutationFunctionTest.java: Could not stat biojava-1.7/tests/org/biojavax/ga/functions/SimpleMutationFunctionTest.java biojava-1.7/tests/org/biojavax/ga/impl/: Could not stat biojava-1.7/tests/org/biojavax/ga/impl biojava-1.7/tests/org/biojavax/ga/impl/SimpleOrganismTest.java: Could not stat biojava-1.7/tests/org/biojavax/ga/impl/SimpleOrganismTest.java biojava-1.7/tests/org/biojavax/ga/impl/SimplePopulationTest.java: Could not stat biojava-1.7/tests/org/biojavax/ga/impl/SimplePopulationTest.java biojava-1.7/tests/org/biojavax/ga/util/: Could not stat biojava-1.7/tests/org/biojavax/ga/util biojava-1.7/tests/org/biojavax/ga/util/GAToolsTest.java: Could not stat biojava-1.7/tests/org/biojavax/ga/util/GAToolsTest.java biojava-1.7/tests/org/biojavax/ga/util/WeightedSetTest.java: Could not stat biojava-1.7/tests/org/biojavax/ga/util/WeightedSetTest.java biojava-1.7/tests/org/biojavax/ontology/: Could not stat biojava-1.7/tests/org/biojavax/ontology biojava-1.7/tests/org/biojavax/ontology/SimpleComparableOntologyTest.java: Could not stat biojava-1.7/tests/org/biojavax/ontology/SimpleComparableOntologyTest.java biojava-1.7/tests/org/biojavax/ontology/SimpleComparableTermTest.java: Could not stat biojava-1.7/tests/org/biojavax/ontology/SimpleComparableTermTest.java biojava-1.7/tests/org/biojavax/ontology/SimpleComparableTripleTest.java: Could not stat biojava-1.7/tests/org/biojavax/ontology/SimpleComparableTripleTest.java biojava-1.7/tests/org/biojavax/SimpleCommentTest.java: Could not stat biojava-1.7/tests/org/biojavax/SimpleCommentTest.java biojava-1.7/tests/org/biojavax/SimpleCrossRefTest.java: Could not stat biojava-1.7/tests/org/biojavax/SimpleCrossRefTest.java biojava-1.7/tests/org/biojavax/SimpleDocRefAuthorTest.java: Could not stat biojava-1.7/tests/org/biojavax/SimpleDocRefAuthorTest.java biojava-1.7/tests/org/biojavax/SimpleDocRefTest.java: Could not stat biojava-1.7/tests/org/biojavax/SimpleDocRefTest.java biojava-1.7/tests/org/biojavax/SimpleNamespaceTest.java: Could not stat biojava-1.7/tests/org/biojavax/SimpleNamespaceTest.java biojava-1.7/tests/org/biojavax/SimpleNoteTest.java: Could not stat biojava-1.7/tests/org/biojavax/SimpleNoteTest.java biojava-1.7/tests/org/biojavax/SimpleRankedCrossRefTest.java: Could not stat biojava-1.7/tests/org/biojavax/SimpleRankedCrossRefTest.java biojava-1.7/tests/org/biojavax/SimpleRankedDocRefTest.java: Could not stat biojava-1.7/tests/org/biojavax/SimpleRankedDocRefTest.java biojava-1.7/tests/org/biojavax/SimpleRichAnnotationTest.java: Could not stat biojava-1.7/tests/org/biojavax/SimpleRichAnnotationTest.java tar: Error exit delayed from previous errors. *** Error code 1 Stop. make: stopped in /usr/ports/biology/biojava
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