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

[James W. MacDonald]

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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