[Bioc-devel] Git transition -- regenerating repositories from svn

Tue Aug 22 22:33:30 CEST 2017

Hi Martin, Nitesh,

thanks for recreating the EBImage repo! I've noticed that even though the
operation helped to fix one commit where the user was previously unknown:

    commit b67438e41b9b7dc62db8c403ee8afd673bd5c0a0
    Author: unknown <jmacdon at med.umich.edu>
    Date:   Fri Apr 21 13:47:14 2006 +0000

    JWM:Added biocViews

    git-svn-id: file:///home/git/
hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/EBImage at 17455
bc3139a8-67e5-0310-9ffc-ced21a209358

there is still a bunch of old commits which match

    [oles at localhost EBImage]$ git log --all --committer="unknown"
--oneline| wc -l
    16

all attributed to

    Author: Patrick Aboyoun <unknown>

So it seems that these are triggered by the unknown email address, not sure
this is intended?

Cheers,
Andrzej

On Tue, Aug 22, 2017 at 10:13 PM, James W. MacDonald <jmacdon at uw.edu> wrote:

> Hi Martin and Nitesh,
>
>
> On Tue, Aug 22, 2017 at 10:09 AM, Martin Morgan <
> martin.morgan at 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/devel
> > opers/how-to/git
>
>
> I delete my clone and create a new one, but the unknown user persists:
>
> $ rm -rf affycoretools
> $ git clone git at 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 <smyth at 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 at 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 at 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
>
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>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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