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

[Martin Morgan]

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

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}}
> 
> _______________________________________________
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