On 08/22/2017 04:33 PM, Andrzej Oleś wrote:
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 <jmac...@med.umich.edu <mailto:jmac...@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@17455 <http://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/EBImage@17455> bc3139a8-67e5-0310-9ffc-ced21a209358


there is still a bunch of old commits which match

[oles@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?

yes, this is the best that we could do with the historical record that we had available (Patrick's email, and a few others, were not recorded in the auxiliary database).

Martin


Cheers,
Andrzej


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

    Hi Martin and Nitesh,


    On Tue, Aug 22, 2017 at 10:09 AM, Martin Morgan <
    martin.mor...@roswellpark.org
    <mailto: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/devel
    > opers/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 <http://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 <mailto: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 <mailto:Bioc-devel@r-project.org>
    mailing list
     >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
    <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
     >>
     >
     >
     > This email message may contain legally privileged
    and/or...{{dropped:2}}
     >
     > _______________________________________________
     > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
    mailing list
     > https://stat.ethz.ch/mailman/listinfo/bioc-devel
    <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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