Never mind. It's all Patrick Aboyoun, for whom I think this should persist.
Jim On Tue, Aug 22, 2017 at 4:13 PM, James W. MacDonald <jmac...@uw.edu> wrote: > Hi Martin and Nitesh, > > > On Tue, Aug 22, 2017 at 10:09 AM, Martin Morgan < > martin.mor...@roswellpark.org> wrote: > >> Thanks for your patience. We updated the repositories below; if you >> cloned one of these repositories, you will need to DELETE your clone, and >> create a new clone. If you have added a remote and pulled from these >> repositories, you will need to redo the sync. See >> https://bioconductor.org/developers/how-to/git > > > I delete my clone and create a new one, but the unknown user persists: > > $ rm -rf affycoretools > $ git clone g...@github.com:/jmacdon/affycoretools.git > Cloning into 'affycoretools'... > Enter passphrase for key '/home/staff/jmacdon/.ssh/id_rsa': > remote: Counting objects: 1865, done. > remote: Compressing objects: 100% (658/658), done. > remote: Total 1865 (delta 1206), reused 1865 (delta 1206), pack-reused 0 > Receiving objects: 100% (1865/1865), 27.93 MiB | 22.36 MiB/s, done. > Resolving deltas: 100% (1206/1206), done. > Checking connectivity... done. > $ cd affycoretools/ > $ git log --all --committer="unknown" --oneline | head > 90098bc Changes to NAMESPACE to import functions from DBI instead of > RSQLite, plus changes to makeImages to allow for directed naming of output > directories. > 8d3b25c Further bugfix for outputRomer. > de970c6 Small bugfix for outputRomer. > 543b3b1 One more commit... > fd1cff3 Final updates to make last commit check. > bcfb73c Several updates. Refactored to move generics to AllGenerics.R. > Converted makeVenn to S4 so it works for MArrayLM as well as DGEGLM > objects. Added ensemblLinks to help make links to Ensembl in HTML tables. > 2d5f066 Forgot to re-run roxygenize on last commit. > 79ce8a6 Changes to getMainProbes to work correctly on Clariom and HTA > arrays. > dbb9143 Small bugfix for plotPCA S4 man page > > Best, > > Jim > > >> >> Thanks, >> >> Martin & Nitesh >> >> ABarray.git >> ACME.git >> AffyCompatible.git >> AffyExpress.git >> AgiMicroRna.git >> AnnotationDbi.git >> AnnotationForge.git >> ArrayExpress.git >> ArrayTools.git >> BAC.git >> BCRANK.git >> BGmix.git >> BSgenome.git >> BUS.git >> BayesPeak.git >> BeadDataPackR.git >> BicARE.git >> BioMVCClass.git >> BioNet.git >> BioSeqClass.git >> Biobase.git >> BiocCaseStudies.git >> Biostrings.git >> BufferedMatrix.git >> BufferedMatrixMethods.git >> CALIB.git >> CGHbase.git >> CGHcall.git >> CGHnormaliter.git >> CGHregions.git >> CMA.git >> CNTools.git >> CNVtools.git >> CORREP.git >> CSAR.git >> Category.git >> ChIPpeakAnno.git >> ChIPseqR.git >> ChIPsim.git >> ChemmineOB.git >> ChemmineR.git >> ChromHeatMap.git >> CoCiteStats.git >> CoGAPS.git >> ConsensusClusterPlus.git >> DChIPRep.git >> DEDS.git >> DEGraph.git >> DEGseq.git >> DESeq.git >> DFP.git >> DNAcopy.git >> Director.git >> DynDoc.git >> EBImage.git >> EBarrays.git >> EasyqpcR.git >> ExpressionView.git >> FlowRepositoryR.git >> GEOmetadb.git >> GEOquery.git >> GEOsubmission.git >> GGBase.git >> GGtools.git >> GLAD.git >> GOFunction.git >> GOSemSim.git >> GOstats.git >> GSEABase.git >> GSEAlm.git >> GSRI.git >> GeneAnswers.git >> GeneMeta.git >> GeneRegionScan.git >> GeneSelectMMD.git >> GeneSelector.git >> GeneticsDesign.git >> GeneticsPed.git >> GenomeGraphs.git >> GenomicFeatures.git >> GenomicRanges.git >> Genominator.git >> GlobalAncova.git >> GraphAT.git >> GraphAlignment.git >> Gviz.git >> HELP.git >> HEM.git >> HTqPCR.git >> Harshlight.git >> Heatplus.git >> HilbertVis.git >> HilbertVisGUI.git >> IRanges.git >> ITALICS.git >> Icens.git >> ImmuneSpaceR.git >> IsoGeneGUI.git >> KCsmart.git >> KEGGgraph.git >> LBE.git >> LMGene.git >> LPE.git >> LPEadj.git >> LiquidAssociation.git >> MANOR.git >> MCRestimate.git >> MEDME.git >> MLInterfaces.git >> MVCClass.git >> MantelCorr.git >> MassArray.git >> MassSpecWavelet.git >> MeasurementError.cor.git >> MergeMaid.git >> Mfuzz.git >> MiChip.git >> MiPP.git >> MinimumDistance.git >> MotIV.git >> NetSAM.git >> OCplus.git >> OLIN.git >> OLINgui.git >> OrderedList.git >> OutlierD.git >> PAnnBuilder.git >> PCpheno.git >> PGSEA.git >> PICS.git >> PING.git >> PLPE.git >> PREDA.git >> PROMISE.git >> PROcess.git >> Pviz.git >> QuasR.git >> RBGL.git >> RBioinf.git >> RCytoscape.git >> RLMM.git >> RNAither.git >> ROC.git >> RPA.git >> RTCA.git >> RankProd.git >> RbcBook1.git >> ReQON.git >> RefPlus.git >> Rgraphviz.git >> Ringo.git >> Rmagpie.git >> RmiR.git >> RpsiXML.git >> Rtreemix.git >> SAGx.git >> SBMLR.git >> SIM.git >> SIMAT.git >> SLGI.git >> SLqPCR.git >> SMAP.git >> SNPchip.git >> SPIA.git >> SRAdb.git >> SRGnet.git >> SSPA.git >> SamSPECTRAL.git >> ScISI.git >> ShortRead.git >> SpeCond.git >> Starr.git >> TargetSearch.git >> TypeInfo.git >> UniProt.ws.git >> VanillaICE.git >> XDE.git >> aCGH.git >> adSplit.git >> affxparser.git >> affy.git >> affyContam.git >> affyILM.git >> affyPLM.git >> affyPara.git >> affyQCReport.git >> affycomp.git >> affycoretools.git >> affyio.git >> affylmGUI.git >> affypdnn.git >> alpine.git >> altcdfenvs.git >> annaffy.git >> annotate.git >> annotationTools.git >> apComplex.git >> aroma.light.git >> arrayMvout.git >> arrayQuality.git >> arrayQualityMetrics.git >> baySeq.git >> beadarraySNP.git >> bgafun.git >> bgx.git >> bioDist.git >> biocGraph.git >> biocViews.git >> biomaRt.git >> bridge.git >> cellHTS2.git >> cghMCR.git >> charm.git >> chimera.git >> chipseq.git >> cleaver.git >> clippda.git >> clusterStab.git >> codelink.git >> convert.git >> copa.git >> crlmm.git >> ctc.git >> customProDB.git >> cycle.git >> daMA.git >> ddCt.git >> diffGeneAnalysis.git >> domainsignatures.git >> dualKS.git >> dyebias.git >> ecolitk.git >> edgeR.git >> eiR.git >> eisa.git >> exomeCopy.git >> explorase.git >> factDesign.git >> fdrame.git >> flagme.git >> flowClust.git >> flowCore.git >> flowFP.git >> flowMeans.git >> flowMerge.git >> flowQ.git >> flowQB.git >> flowTrans.git >> flowUtils.git >> flowViz.git >> fmcsR.git >> frma.git >> frmaTools.git >> gaga.git >> gaggle.git >> gcrma.git >> genArise.git >> geneRecommender.git >> genefilter.git >> geneplotter.git >> genoCN.git >> genomeIntervals.git >> genomes.git >> genphen.git >> girafe.git >> globaltest.git >> goProfiles.git >> goTools.git >> goseq.git >> gpls.git >> graph.git >> hopach.git >> hyperdraw.git >> hypergraph.git >> iChip.git >> idiogram.git >> impute.git >> iontree.git >> iterativeBMA.git >> iterativeBMAsurv.git >> keggorthology.git >> lapmix.git >> leeBamViews.git >> limma.git >> limmaGUI.git >> logicFS.git >> logitT.git >> lumi.git >> mBPCR.git >> maCorrPlot.git >> maSigPro.git >> maanova.git >> macat.git >> made4.git >> maigesPack.git >> makecdfenv.git >> marray.git >> mdqc.git >> metaArray.git >> metahdep.git >> methVisual.git >> methylumi.git >> miRNApath.git >> microRNA.git >> minet.git >> monocle.git >> multiscan.git >> multtest.git >> nem.git >> nnNorm.git >> nudge.git >> occugene.git >> oligo.git >> oligoClasses.git >> oneChannelGUI.git >> panp.git >> parody.git >> pathRender.git >> pcaMethods.git >> pcot2.git >> pdInfoBuilder.git >> pdmclass.git >> pepStat.git >> pepXMLTab.git >> pickgene.git >> pint.git >> pkgDepTools.git >> plateCore.git >> plgem.git >> plier.git >> plw.git >> ppiStats.git >> prada.git >> preprocessCore.git >> proBAMr.git >> puma.git >> qpcrNorm.git >> qpgraph.git >> quantsmooth.git >> qvalue.git >> r3Cseq.git >> rGADEM.git >> rHVDM.git >> rMAT.git >> rTRM.git >> rTRMui.git >> rama.git >> rbsurv.git >> reb.git >> rhdf5.git >> rsbml.git >> rtracklayer.git >> safe.git >> sagenhaft.git >> segmentSeq.git >> seqLogo.git >> sigPathway.git >> siggenes.git >> simpleaffy.git >> sizepower.git >> snapCGH.git >> spikeLI.git >> spkTools.git >> splicegear.git >> splots.git >> spotSegmentation.git >> sscore.git >> ssize.git >> stepNorm.git >> systemPipeR.git >> tigre.git >> tilingArray.git >> timecourse.git >> tkWidgets.git >> topGO.git >> tspair.git >> twilight.git >> tximport.git >> vbmp.git >> weaver.git >> webbioc.git >> widgetTools.git >> xcms.git >> xmapbridge.git >> xps.git >> yaqcaffy.git >> >> >> >> On 08/21/2017 12:00 PM, Martin Morgan wrote: >> >>> Hi git transitioners -- >>> >>> We'd like to regenerate git repositories from svn. This is because some >>> svn user ids were mapped to 'unknown' git users, so that contributors would >>> not be credited accurately. This will invalidate any local clones made >>> from git.bioconductor.org. >>> >>> Our plan is to regenerate all git repositories EXCEPT those that have >>> been modified when we are ready (probably tomorrow morning). Modified >>> repositories that we would NOT regenerate, based on current commits, are >>> listed below; repositories modified between now and when we are ready to >>> update would also NOT be regenerated: >>> >>> beadarray BiocStyle CAMERA Cardinal CEMiTool ChemmineR cydar cytofkit >>> derfinder derfinderHelper derfinderPlot DmelSGI DOSE EBImage ELMER >>> ensembldb FamAgg gcapc GenVisR ggtree GOexpress gQTLstats GWASTools isomiRs >>> karyoploteR LOBSTAHS motifcounter piano Rdisop REMP Rhdf5lib rnaseqcomp >>> seqplots systemPipeR TCGAbiolinks TCGAbiolinksGUI vsn >>> >>> >>> For a little more detail, the problem is manifest as 'unknown' authors >>> in a git commit, e.g., in Biobase from svn user 'jmc' >>> >>> commit b5ae43bc8aae967b80062da13e5085a6a305b274 >>> Author: unknown <unknown> >>> Date: Fri Dec 7 15:17:06 2001 +0000 >>> >>> fixed the arguments to 'show' methods >>> >>> >>> A more common problem is that the git author 'name' is 'unknown', as in >>> this limma commit >>> >>> commit 5910dc34a952a72816ada787d3f2c849edf48a95 >>> Author: unknown <sm...@wehi.edu.au> >>> Date: Tue Jul 25 07:23:39 2017 +0000 >>> >>> >>> >>> The problem primarily affects users with svn accounts from the earlier >>> part of Bioconductor's svn history, and stems from incomplete historical >>> records about the user name associated with svn accounts (this information >>> is not stored in svn per se). >>> >>> Please feel free to respond here if your package is listed above but you >>> would like it to be regenerated anyway; remember that you will loose any >>> commits made, and invalidate your local repository. >>> >>> Sorry for the inconvenience, >>> >>> Martin >>> >>> >>> This email message may contain legally privileged and/or...{{dropped:2}} >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> >> This email message may contain legally privileged and/or...{{dropped:2}} >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
