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

[James W. MacDonald]

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 <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/developers/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
>



-- 
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]]