setup
checks.i686-linux.kent
· build #5
· raw
1this derivation will be built:2 /nix/store/l9mfa7l8xvd0842f3f36zkxg9h036bvx-kent-404.drv3these 2 paths will be fetched (56.7 KiB download, 299.7 KiB unpacked):4 /nix/store/xlc0xvxfa1qhs6qzvvdmlgpkn2psazjq-mariadb-connector-c-3.2.5-dev5 /nix/store/d5q43ssc7l61nrvqw3z77iwpb87aq3si-util-linux-minimal-2.38.1-dev6error: Cannot build '/nix/store/l9mfa7l8xvd0842f3f36zkxg9h036bvx-kent-404.drv'.7 Reason: builder failed with exit code 1.8 Output paths:9 /nix/store/7i888y011shcj68cnigk3l933d42fp90-kent-40410 Last 25 log lines:11 > gcc -O -g -fPIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_i686 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/nix/store/yc42mb1qgf4b9p66mgs3smnw59wq29k4-libpng-apng-1.6.37-dev/include/libpng16 -I/nix/store/xlc0xvxfa1qhs6qzvvdmlgpkn2psazjq-mariadb-connector-c-3.2.5-dev/include -I/nix/store/xlc0xvxfa1qhs6qzvvdmlgpkn2psazjq-mariadb-connector-c-3.2.5-dev/include/mysql -o gencodeTranscriptionSupportLevel.o -c gencodeTranscriptionSupportLevel.c12 > gcc -O -g -fPIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_i686 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/nix/store/yc42mb1qgf4b9p66mgs3smnw59wq29k4-libpng-apng-1.6.37-dev/include/libpng16 -I/nix/store/xlc0xvxfa1qhs6qzvvdmlgpkn2psazjq-mariadb-connector-c-3.2.5-dev/include -I/nix/store/xlc0xvxfa1qhs6qzvvdmlgpkn2psazjq-mariadb-connector-c-3.2.5-dev/include/mysql -o gencodeTranscriptSource.o -c gencodeTranscriptSource.c13 > gcc -O -g -fPIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_i686 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/nix/store/yc42mb1qgf4b9p66mgs3smnw59wq29k4-libpng-apng-1.6.37-dev/include/libpng16 -I/nix/store/xlc0xvxfa1qhs6qzvvdmlgpkn2psazjq-mariadb-connector-c-3.2.5-dev/include -I/nix/store/xlc0xvxfa1qhs6qzvvdmlgpkn2psazjq-mariadb-connector-c-3.2.5-dev/include/mysql -o gencodeTranscriptSupport.o -c gencodeTranscriptSupport.c14 > gcc -O -g -fPIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_i686 -DUSE_HIC -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I../../htslib -I/include -I/nix/store/yc42mb1qgf4b9p66mgs3smnw59wq29k4-libpng-apng-1.6.37-dev/include/libpng16 -I/nix/store/xlc0xvxfa1qhs6qzvvdmlgpkn2psazjq-mariadb-connector-c-3.2.5-dev/include -I/nix/store/xlc0xvxfa1qhs6qzvvdmlgpkn2psazjq-mariadb-connector-c-3.2.5-dev/include/mysql -o gencodeToUniProt.o -c gencodeToUniProt.c15 > cd straw && make straw.o16 > make[2]: Entering directory '/build/source/src/hg/lib/straw'17 > g++ straw.cpp -g -c -lz -std=c++11 -lcurl -o ../straw.o18 > make[2]: Leaving directory '/build/source/src/hg/lib/straw'19 > ar rcus ../../lib/i686/jkhgap.a acemblyClass.o adjacency.o affyAllExonProbe.o affyAtlas.o affy10KDetails.o affy120KDetails.o affyOffset.o affyPairs.o agp.o agpFrag.o agpGap.o alignSeqSizes.o altGraph.o altGraphX.o ancientRref.o annoFormatVep.o annoGratorGpVar.o annoGrateWigDb.o annoStreamDb.o annoStreamDbFactorSource.o annoStreamDbPslPlus.o annoStreamWig.o api.o atomDb.o autoUpgrade.o axtInfo.o axtLib.o bactigPos.o hgBam.o barChartBed.o barChartCategory.o barChartUi.o barChartData.o barChartSample.o baseMaskCommon.o bdgpExprLink.o bdgpGeneInfo.o bed.o bed5FloatScore.o bed5Pval.o bed6FloatScore.o bed8Attrs.o bed12Source.o bed12wSeq.o bedCart.o bgiGeneInfo.o bgiGeneSnp.o bgiSnp.o bigBedFind.o bigBedLabel.o bigDbSnp.o bigGenePred.o bigPsl.o bigTransMap.o bioImage.o blastTab.o blastzNet.o blatServers.o borf.o borkPseudoHom.o botDelay.o cart.o cartDb.o cartJson.o cartTrackDb.o cdsEvidence.o cdsOrtho.o cdsPick.o cdsSpec.o ccdsInfo.o ccdsNotes.o ccdsGeneMap.o celeraCoverage.o celeraDupPositive.o cgapSage/cgapSage.o cgapSage/cgapSageLib.o cgh.o chainCart.o chainDb.o chainLink.o chainNet.o chainNetDbLoad.o chicken13kInfo.o chromBins.o chromAlias.o chr18deletions.o chromGraph.o chromGraphFactory.o chromInfo.o chromInserts.o chromKeeper.o clonePos.o codeBlast.o codeBlastScore.o cogs.o cogsxra.o columnInfo.o contigAcc.o coordConv.o cnpIafrate.o cnpIafrate2.o cnpLocke.o cnpRedon.o cnpSebat.o cnpSebat2.o cnpSharp2.o cnpSharpCutoff.o cnpSharpSample.o cnpSharp.o cpgIsland.o cpgIslandExt.o ctgPos.o ctgPos2.o customComposite.o bedDetail.o cgiApoptosis.o customAdjacency.o customFactory.o customPp.o customTrack.o cutter.o cv.o cytoBand.o dbDb.o dbRIP.o dbSnpDetails.o dbSnpRs.o defaultDb.o delConrad2.o delHinds2.o dgv.o dgvPlus.o dless.o dnaMotifSql.o dnaMarkovSql.o dnaProbe.o dv.o dvBed.o dvXref2.o easyGene.o ec.o ecCode.o ecAttribute.o ecAttributeCode.o encode/encodeErge.o encode/encodeErgeHssCellLines.o encode/encodeHapMapAlleleFreq.o encode/encodeIndels.o encode/encodePeak.o encode/encodeRegionInfo.o encode/encodeRegionInfoCustom.o encode/encodeRna.o encode/encodeStanfordPromoters.o encode/encodeStanfordPromotersAverage.o encode/pairedTagAlign.o encode/peptideMapping.o encode/tagAlign.o encode/wgEncodeGencodeAttrs.o encode/wgEncodeGencodeExonSupport.o encode/wgEncodeGencodeEntrezGene.o encode/wgEncodeGencodeTag.o encode/wgEncodeGencodeGeneSymbol.o encode/wgEncodeGencodePdb.o encode/wgEncodeGencodePubMed.o encode/wgEncodeGencodeRefSeq.o encode/wgEncodeGencodeGeneSource.o encode/wgEncodeGencodeTranscriptSource.o encode/wgEncodeGencodeTranscriptSupport.o encode/wgEncodeGencodeTranscriptionSupportLevel.o encode/wgEncodeGencodeUniProt.o encode/wgEncodeGencodePolyAFeature.o encode/wgEncodeGencodeAnnotationRemark.o encode/wgEncodeCell.o encode/encodeExp.o encode3/encode2Manifest.o encode3/encode3Valid.o ensFace.o ensInfo.o ensPhusionBlast.o ensXRefZfish.o est3.o estOrientInfo.o estPair.o exoFish.o expData.o expRecord.o exprBed.o facetField.o factorSource.o fbTables.o featureBits.o fileUi.o findKGAlias.o findKGProtAlias.o fishClones.o flyBase2004Xref.o flyBaseSwissProt.o flyreg.o flyreg2.o gbExtFile.o gbWarn.o gbMiscDiff.o gbProtAnn.o gcPercent.o gbSeq.o genbank.o genbankBlackList.o gencodeGeneClass.o gencodeIntron.o genMapDb.o geneBands.o geneCheck.o geneCheckDetails.o geneCheckWidget.o geneGraph.o genePred.o genePredReader.o geneSimilarities.o genoLay.o genomeRangeTreeFile.o genomicDups.o genomicSuperDups.o geoMirror.o ggCluster.o ggDbIo.o ggDump.o ggGraph.o ggMrnaAli.o ggTypes.o glDbRep.o goa.o goaPart.o googleAnalytics.o gpFx.o growthCondition.o grp.o gtexAse.o gtexBoxplot.o gtexEqtlCluster.o gtexInfo.o gtexDonor.o gtexGeneBed.o gtexSample.o gtexSampleData.o gtexTissue.o gtexTissueData.o gtexTissueMedian.o gtexUi.o gwasCatalog.o hAnno.o haplotypes.o hapmapAllelesOrtho.o hapmapAllelesSummary.o hapmapPhaseIIISummary.o hapmapSnps.o hapmapSnpsCombined.o hashJoin.o hCommon.o hCytoBand.o hdb.o hgColors.o hgConfig.o hgExp.o hgFind.o hgFindSpec.o hgFindSpecCustom.o hgHgvs.o hgHgvsParse.o hgGene.o hic.o hicUi.o hgMaf.o hgRelate.o hgSeq.o hgdpGeo.o hPrint.o hVarSubst.o hvGfx.o HInv.o hubConnect.o hubSearchText.o hui.o humanParalog.o hubPublic.o imageClone.o indelShift.o interact.o interactUi.o isochores.o ispyTables.o itemAttr.o itemConf.o itemDetailsHtml.o jalview.o jaxOrtholog.o jaxQTL.o jaxQTL3.o jksql.o joiner.o jsHelper.o kg1ToKg2.o jgiGene.o joinMixer.o kgAlias.o kgColor.o kgProtAlias.o kgXref.o knownInfo.o knownMore.o knownToSuper.o lav.o ld.o ld2.o lfs.o liftOver.o liftOverChain.o liftUp.o llaInfo.o longRange.o lrg.o lsSnpPdb.o lsSnpPdbChimera.o mafFrames.o mafGene.o mafSummary.o makeItemsItem.o mammalPsg.o mapSts.o mathWig.o mcnBreakpoints.o mdb.o metaChromGraph.o microarray.o minChromSize.o minGeneInfo.o mrnaMisMatch.o mouseOrtho.o mouseSyn.o mouseSynWhd.o mysqlTableStatus.o ncbiRefLink.o ncbiRefSeqLink.o netAlign.o netCart.o nonCodingUi.o omimTitle.o ooUtils.o orthoAlleles.o pal.o pbStamp.o pcrResult.o pepPred.o peptideAtlasPeptide.o plasEndPairs.o polyGenotype.o protFeat.o pscreen.o pseudoGeneLink.o pslReader.o pslWScore.o putaInfo.o qaSeq.o rangeTreeFile.o rankProp.o recombRate.o recombRateRat.o recombRateMouse.o refLink.o refSeqStatus.o rgdQtl.o riken.o rhMapZfishInfo.o rikenBest.o rikenCluster.o rmskOut.o rmskAlign.o rmskJoined.o rmskOut2.o rnaFold.o rnaGene.o rnaGroup.o rnaHybridization.o rnaPLFold.o tRNAs.o gbRNAs.o snoRNAs.o lowelabPfamHit.o lowelabArkinOperonScore.o lowelabTIGROperonScore.o rnaSecStr.o tfbsConsFactors.o roughAli.o transMapStuff.o transMapInfo.o transMapGene.o transMapSrc.o sage.o sageCounts.o sageExp.o samAlignment.o sample.o sanger22extra.o sangerGene.o sangerGeneToWBGeneID.o sargassoSeaXra.o scopDes.o scoredRef.o search.o seqWindow.o sessionThumbnail.o sgdAbundance.o sgdClone.o sgdDescription.o sgdOther.o simpleNucDiff.o simpleRepeat.o snakeUi.o snp.o snp125.o snp125CodingCoordless.o snp132Ext.o snpExceptions.o snpFasta.o snpMap.o snpTmp.o snpUi.o snp125Exceptions.o snp125Ui.o softPromoter.o softberryHom.o soTerm.o spDb.o splignAlign.o sqlSanity.o stanMad.o stsAlias.o stsInfo.o stsInfo2.o stsInfoMouse.o stsInfoMouseNew.o stsInfoRat.o stsMap.o stsMapMouse.o stsMapMouseNew.o stsMapRat.o stsMarker.o suggest.o switchDbTss.o synMap.o synteny100000.o syntenyBerk.o syntenySanger.o sqlProg.o tfbsCons.o tfbsConsSites.o tablesTables.o tableDescriptions.o tableStatus.o targetDb.o tfbsConsMap.o tagRepo.o taxonDivision.o taxonGeneticCode.o taxonName.o taxonNode.o taxonXref.o tigrCmrGene.o tigrOperon.o tilingPath.o traceInfo.o trackDb.o trackDbCustom.o trackDbCache.o trackHub.o trackLayout.o trackTable.o trackVersion.o trashDir.o transRegCode.o transRegCodeCondition.o transRegCodeProbe.o txAliDiff.o txCluster.o txCommon.o txEdgeBed.o txEdgeOrtho.o txGraph.o txInfo.o txRnaAccs.o ucscRetroInfo.o ucscRetroOrtho.o variant.o variantProjector.o vcfUi.o vegaInfo.o vegaInfoZfish.o visiGene.o vntr.o wabAli.o web.o ncRna.o wgRna.o wigAsciiToBinary.o wigDataStream.o wiggle.o wiggleCart.o wiggleUtils.o wikiLink.o wikiTrack.o yaleGencodeAssoc.o zdobnovSynt.o oreganno.o oregannoUi.o gvUi.o gv.o omicia.o protVar.o pgSnp.o alignInfo.o cddInfo.o loweutils.o cddDesc.o arCOGs.o arcogdesc.o geneTree.o megablastInfo.o pgPhenoAssoc.o pgSiftPred.o pgPolyphenPred.o userRegions.o variome.o gencodeAnnotationRemark.o gencodeAttrs.o gencodeToEntrezGene.o gencodeExonSupport.o gencodeGeneSource.o gencodeToGeneSymbol.o gencodeToPdb.o gencodeToPubMed.o gencodeToRefSeq.o gencodeTag.o gencodeTranscriptionSupportLevel.o gencodeTranscriptSource.o gencodeTranscriptSupport.o gencodeToUniProt.o straw.o20 > ar: `u' modifier ignored since `D' is the default (see `U')21 > make[1]: Leaving directory '/build/source/src/hg/lib'22 > cd optimalLeaf && make23 > make[1]: Entering directory '/build/source/src/optimalLeaf'24 > g++ -c -g Tree.cc25 > g++ -c -g Leaf.cc26 > g++ -c -g readFile.cc27 > g++ -c -g SimMat.cc28 > g++ -c -g bestArr.cc29 > mkdir i68630 > ar rcus ../lib/i686/optimalLeaf.a Tree.o Leaf.o readFile.o SimMat.o bestArr.o31 > ar: `u' modifier ignored since `D' is the default (see `U')32 > make[1]: Leaving directory '/build/source/src/optimalLeaf'33 > ar rcus ../lib/i686/jkOwnLib.a bandExt.o crudeali.o ffAliHelp.o ffSeedExtend.o fuzzyFind.o genoFind.o gfBlatLib.o gfClientLib.o gfInternal.o gfOut.o gfPcrLib.o gfWebLib.o ooc.o patSpace.o splix.o supStitch.o trans3.o xenbig.o xensmall.o34 > ar: `u' modifier ignored since `D' is the default (see `U')35 > cp: cannot stat '../lib/x86_64/jkOwnLib.a': No such file or directory36 For full logs, run:37 nix log /nix/store/l9mfa7l8xvd0842f3f36zkxg9h036bvx-kent-404.drv