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Bioc-devel April 2014

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Wednesday, April 30, 2014 10 emails
Michael Lawrence r+w permissions in release branches Kasper Daniel Hansen r+w permissions in release branches Martin Morgan r+w permissions in release branches Kasper Daniel Hansen r+w permissions in release branches Ryan Additional summarizeOverlaps counting modes for ChIP-Seq Valerie Obenchain Additional summarizeOverlaps counting modes for ChIP-Seq Ryan Additional summarizeOverlaps counting modes for ChIP-Seq Lance Parsons Gviz AnnotationTrack ylim patch Hervé Pagès rbind,DataFrame vs rbind.data.frame Michael Lawrence rbind,DataFrame vs rbind.data.frame
Tuesday, April 29, 2014 3 emails
Hervé Pagès rbind,DataFrame vs rbind.data.frame Martin Morgan Rsamtools applyPileups function not merging positions from multiple files if not identical Jonathon Hill Rsamtools applyPileups function not merging positions from multiple files if not identical
Monday, April 28, 2014 2 emails
Valerie Obenchain Bug in as.data.frame method for RangedData? Kevin Ushey Bug in as.data.frame method for RangedData?
Saturday, April 26, 2014 1 email
Ryan Missing seqinfo method for BamFileList?
Friday, April 25, 2014 5 emails
Martin Morgan Missing seqinfo method for BamFileList? Ryan Missing seqinfo method for BamFileList? Martin Morgan CITATION on the Bioc package landing page? Hervé Pagès r+w permissions in release branches Hervé Pagès 'memory not mapped' in trimLRpatterns
Thursday, April 24, 2014 13 emails
Michael Lawrence CITATION on the Bioc package landing page? Vincent Carey CITATION on the Bioc package landing page? Wolfgang Huber CITATION on the Bioc package landing page? Dan Tenenbaum git svn bridge is broken Mike git svn bridge is broken Tengfei Yin IRanges:::safeExplode Steve Lianoglou r+w permissions in release branches Gabriel Becker error in summary method for KEGGHyperGResult Wolfgang Huber r+w permissions in release branches James W. MacDonald error in summary method for KEGGHyperGResult Gabriel Becker error in summary method for KEGGHyperGResult Kasper Daniel Hansen r+w permissions in release branches Wolfgang Huber r+w permissions in release branches
Wednesday, April 23, 2014 10 emails
Josef Spidlen Dependency on windowing systems in the flowCore package Hervé Pagès IRanges:::safeExplode Tengfei Yin IRanges:::safeExplode Kevin Ushey Lazy evaluation and S4 methods Michael Lawrence Lazy evaluation and S4 methods Kevin Ushey Lazy evaluation and S4 methods Michael Lawrence Lazy evaluation and S4 methods Kevin Ushey Lazy evaluation and S4 methods Martin Morgan r+w permissions in release branches Martin Morgan Rsamtools applyPileups function not merging positions from multiple files if not identical
Tuesday, April 22, 2014 19 emails
Hervé Pagès metadata() in BiocGenerics? Davide Risso Package vignette and knitr Mike Dependency on windowing systems in the flowCore package Dan Tenenbaum Package vignette and knitr Kieran O'Neill Dependency on windowing systems in the flowCore package Davide Risso Package vignette and knitr Kasper Daniel Hansen r+w permissions in release branches Julian Gehring r+w permissions in release branches Wolfgang Huber r+w permissions in release branches Michael Stadler 'memory not mapped' in trimLRpatterns Jonathon Hill Rsamtools applyPileups function not merging positions from multiple files if not identical Julian Gehring r+w permissions in release branches Alejandro Reyes r+w permissions in release branches Andrzej Oleś r+w permissions in release branches Martin Morgan BiocUpgrades updates to devel instead of stable Julian Gehring BiocUpgrades updates to devel instead of stable Kasper Daniel Hansen r+w permissions in release branches Julian Gehring BiocUpgrades updates to devel instead of stable Alejandro Reyes r+w permissions in release branches
Monday, April 21, 2014 4 emails
Martin Morgan Rsamtools applyPileups function not merging positions from multiple files if not identical Henrik Bengtsson Rsamtools: Is extdata/ex1.bam.bai outdated? Jonathon Hill Rsamtools applyPileups function not merging positions from multiple files if not identical Martin Morgan Rsamtools: Is extdata/ex1.bam.bai outdated?
Sunday, April 20, 2014 7 emails
Tim Triche, Jr. suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38 Hervé Pagès suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38 Tim Triche, Jr. suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38 Martin Morgan suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38 Martin Morgan suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38 Hervé Pagès suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38 Michael Lawrence suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38
Friday, April 18, 2014 6 emails
Henrik Bengtsson Rsamtools: Is extdata/ex1.bam.bai outdated? Dan Tenenbaum New package version and BiocCheck Mike Dependency on windowing systems in the flowCore package Dan Tenenbaum New package version and BiocCheck Dan Gatti New package version and BiocCheck Martin Morgan Dependency on windowing systems in the flowCore package
Thursday, April 17, 2014 8 emails
Mike Dependency on windowing systems in the flowCore package Marc Carlson strange spam from biocbuild Taku Tokuyasu Apparent error in illuminaHumanv4.db Hervé Pagès S4Vectors package Steve Lianoglou BiocUpgrades updates to devel instead of stable Julian Gehring BiocUpgrades updates to devel instead of stable Michael Lawrence metadata() in BiocGenerics? Vincent Carey metadata() in BiocGenerics?
Wednesday, April 16, 2014 10 emails
Hervé Pagès metadata() in BiocGenerics? Mike Dependency on windowing systems in the flowCore package Michael Lawrence suggestion about bioconductor package-- BSgenome.Hsapiens.NCBI.GRCh38 Hervé Pagès suggestion about bioconductor package-- BSgenome.Hsapiens.NCBI.GRCh38 Michael Lawrence suggestion about bioconductor package-- BSgenome.Hsapiens.NCBI.GRCh38 Hervé Pagès suggestion about bioconductor package-- BSgenome.Hsapiens.NCBI.GRCh38 Gabriel Becker Packaging a medium/large project Julian Gehring Packaging a medium/large project Julian Gehring Packaging a medium/large project ushi Packaging a medium/large project
Tuesday, April 15, 2014 7 emails
Dan Tenenbaum Can\'t load new BioC packages Nicolas Delhomme biocLite “no packages in repository” error Nicolas Delhomme Can\'t load new BioC packages Dan Tenenbaum biocLite “no packages in repository” error Nicolas Delhomme biocLite “no packages in repository” error Dan Tenenbaum biocLite “no packages in repository” error Dan Tenenbaum biocLite “no packages in repository” error
Monday, April 14, 2014 1 email
Dan Tenenbaum Bioconductor 2.14 is released
Friday, April 11, 2014 8 emails
Peter Hickey Restrictions on findOverlaps parameters with SummarizedExperiment objects Dan Tenenbaum BioC 2.14 branch created Martin Morgan Restrictions on findOverlaps parameters with SummarizedExperiment objects Dan Tenenbaum Important: Bioconductor 2.14 branch to be created today Dan Tenenbaum Important: Bioconductor 2.14 branch to be created today Tengfei Yin seqlevelsStyle<- doesn't work for GRanges object Hervé Pagès seqlevelsStyle<- doesn't work for GRanges object Laurent Gatto compare generics
Thursday, April 10, 2014 15 emails
Peter Hickey Restrictions on findOverlaps parameters with SummarizedExperiment objects Kieran O'Neill Dependency on windowing systems in the flowCore package Hervé Pagès compare generics Kevin Ushey Dependency on windowing systems in the flowCore package Kasper Daniel Hansen Dependency on windowing systems in the flowCore package Kevin Ushey Dependency on windowing systems in the flowCore package Tengfei Yin seqlevelsStyle<- doesn't work for GRanges object Tengfei Yin seqlevelsStyle<- doesn't work for GRanges object Kieran O'Neill Dependency on windowing systems in the flowCore package Dan Tenenbaum Dependency on windowing systems in the flowCore package Kieran O'Neill Dependency on windowing systems in the flowCore package Gustavo H. Esteves Old version of packages Dan Tenenbaum Old version of packages Vincent Carey metadata() in BiocGenerics? Gustavo H. Esteves Old version of packages
Wednesday, April 9, 2014 8 emails
Michael Stadler "[[<-" method dispatch and GenomicRanges Laurent Gatto compare generics Valerie Obenchain restrictToSNV for VCF Hervé Pagès "[[<-" method dispatch and GenomicRanges Vincent Carey "[[<-" method dispatch and GenomicRanges Dan Du Commit Problem Morganella Sandro Commit Problem Michael Stadler "[[<-" method dispatch and GenomicRanges
Tuesday, April 8, 2014 8 emails
Dan Tenenbaum git-svn bridge down? Dan Tenenbaum git-svn bridge down? Dan Tenenbaum git-svn bridge down? Dan Tenenbaum git-svn bridge down? Neumann, Steffen git-svn bridge down? Julian Gehring git-svn bridge down? Charles Plessy No propagation from the GitHub bridge (clonotypeR package). Julian Gehring git-svn bridge down?
Monday, April 7, 2014 6 emails
Luo Weijun unexpected build and check error Dan Tenenbaum Preparing package release notes Dan Tenenbaum git-svn bridge down? Julian Gehring git-svn bridge down? Dan Tenenbaum git-svn bridge down? Julian Gehring git-svn bridge down?
Sunday, April 6, 2014 11 emails
Hervé Pagès rownames in SummerizedExperiments Simon Anders rownames in SummerizedExperiments Michael Lawrence rownames in SummerizedExperiments Dan Tenenbaum Bioconductor packages for R-3.1.0 beta on OSX 10.9 Diego Diez Bioconductor packages for R-3.1.0 beta on OSX 10.9 Dan Tenenbaum unexpected build and check error Luo Weijun unexpected build and check error Martin Morgan rownames in SummerizedExperiments Michael Lawrence rownames in SummerizedExperiments Simon Anders rownames in SummerizedExperiments Michael Lawrence rownames in SummerizedExperiments
Saturday, April 5, 2014 3 emails
Martin Morgan unexpected build and check error Simon Anders rownames in SummerizedExperiments Simon Anders rownames in SummerizedExperiments
Friday, April 4, 2014 5 emails
Luo Weijun unexpected build and check error Dan Tenenbaum Bioconductor support for R-3.1.0 on Mavericks (Mac OS X 10.9) Martin Morgan A question on IRanges package Dan Tenenbaum Bioconductor packages for R-3.1.0 beta on OSX 10.9 Diego Diez Bioconductor packages for R-3.1.0 beta on OSX 10.9
Thursday, April 3, 2014 18 emails
Hervé Pagès Subsetting Lists by Lists Hervé Pagès preservation of names by translate,DNAStringSet Gabriel Becker A question on IRanges package Yuan Luo A question on IRanges package Yuan Luo A question on IRanges package Martin Morgan A question on IRanges package Michael Lawrence A question on IRanges package Yuan Luo A question on IRanges package Michael Lawrence preservation of names by translate,DNAStringSet Michael Lawrence A question on IRanges package Yuan Luo A question on IRanges package Michael Lawrence A question on IRanges package Michael Lawrence renameSeqlevels name matching Arora, Sonali renameSeqlevels name matching Michael Lawrence renameSeqlevels name matching Yuan Luo A question on IRanges package Michael Lawrence Conflicting definitions for function redefined as S4 generics Ulrich Bodenhofer Conflicting definitions for function redefined as S4 generics
Tuesday, April 1, 2014 23 emails
Michael Lawrence Subsetting Lists by Lists Tim Triche, Jr. Subsetting Lists by Lists Hervé Pagès Subsetting Lists by Lists Hervé Pagès Subsetting Lists by Lists Hervé Pagès Subsetting Lists by Lists Michael Lawrence Subsetting Lists by Lists Hervé Pagès Subsetting Lists by Lists Hervé Pagès Subsetting Lists by Lists Tim Triche, Jr. Subsetting Lists by Lists Arora, Sonali beadarray warning (seqlevelsStyle?) Arora, Sonali beadarray warning (seqlevelsStyle?) Ryan Subsetting Lists by Lists Dan Tenenbaum BiocCheck: Allowed formats for vignette source Julian Gehring BiocCheck: Allowed formats for vignette source Valerie Obenchain Bioconductor newsletter: April 2014 Cook, Malcolm Subsetting Lists by Lists Cook, Malcolm Bioconductor newsletter: April 2014 Valerie Obenchain Bioconductor newsletter: April 2014 Michael Lawrence Subsetting Lists by Lists Bernd Fischer svn repository for data experiment packages now having branches too Laurent Gatto svn repository for data experiment packages now having branches too Martin Rijlaarsdam beadarray warning (seqlevelsStyle?) Mark Dunning beadarray warning (seqlevelsStyle?)