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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