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Bioc-devel April 2014

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"[[<-" method dispatch and GenomicRanges

4 msgs
Michael Stadler "[[<-" method dispatch and GenomicRanges Apr 9, 2014 Vincent Carey "[[<-" method dispatch and GenomicRanges Apr 9, 2014 Hervé Pagès "[[<-" method dispatch and GenomicRanges Apr 9, 2014 Michael Stadler "[[<-" method dispatch and GenomicRanges Apr 9, 2014

'memory not mapped' in trimLRpatterns

2 msgs
Michael Stadler 'memory not mapped' in trimLRpatterns Apr 22, 2014 Hervé Pagès 'memory not mapped' in trimLRpatterns Apr 25, 2014

A question on IRanges package

11 msgs
Yuan Luo A question on IRanges package Apr 3, 2014 Michael Lawrence A question on IRanges package Apr 3, 2014 Yuan Luo A question on IRanges package Apr 3, 2014 Michael Lawrence A question on IRanges package Apr 3, 2014 Yuan Luo A question on IRanges package Apr 3, 2014 Michael Lawrence A question on IRanges package Apr 3, 2014 Martin Morgan A question on IRanges package Apr 3, 2014 Yuan Luo A question on IRanges package Apr 3, 2014 Yuan Luo A question on IRanges package Apr 3, 2014 Gabriel Becker A question on IRanges package Apr 3, 2014 Martin Morgan A question on IRanges package Apr 4, 2014

Additional summarizeOverlaps counting modes for ChIP-Seq

3 msgs
Ryan Additional summarizeOverlaps counting modes for ChIP-Seq Apr 30, 2014 Valerie Obenchain Additional summarizeOverlaps counting modes for ChIP-Seq Apr 30, 2014 Ryan Additional summarizeOverlaps counting modes for ChIP-Seq Apr 30, 2014

Apparent error in illuminaHumanv4.db

1 msg
Taku Tokuyasu Apparent error in illuminaHumanv4.db Apr 17, 2014

BioC 2.14 branch created

1 msg
Dan Tenenbaum BioC 2.14 branch created Apr 11, 2014

BiocCheck: Allowed formats for vignette source

2 msgs
Julian Gehring BiocCheck: Allowed formats for vignette source Apr 1, 2014 Dan Tenenbaum BiocCheck: Allowed formats for vignette source Apr 1, 2014

BiocUpgrades updates to devel instead of stable

5 msgs
Julian Gehring BiocUpgrades updates to devel instead of stable Apr 17, 2014 Steve Lianoglou BiocUpgrades updates to devel instead of stable Apr 17, 2014 Julian Gehring BiocUpgrades updates to devel instead of stable Apr 22, 2014 Julian Gehring BiocUpgrades updates to devel instead of stable Apr 22, 2014 Martin Morgan BiocUpgrades updates to devel instead of stable Apr 22, 2014

Bioconductor 2.14 is released

1 msg
Dan Tenenbaum Bioconductor 2.14 is released Apr 14, 2014

Bioconductor newsletter: April 2014

3 msgs
Valerie Obenchain Bioconductor newsletter: April 2014 Apr 1, 2014 Cook, Malcolm Bioconductor newsletter: April 2014 Apr 1, 2014 Valerie Obenchain Bioconductor newsletter: April 2014 Apr 1, 2014

Bioconductor packages for R-3.1.0 beta on OSX 10.9

4 msgs
Diego Diez Bioconductor packages for R-3.1.0 beta on OSX 10.9 Apr 4, 2014 Dan Tenenbaum Bioconductor packages for R-3.1.0 beta on OSX 10.9 Apr 4, 2014 Diego Diez Bioconductor packages for R-3.1.0 beta on OSX 10.9 Apr 6, 2014 Dan Tenenbaum Bioconductor packages for R-3.1.0 beta on OSX 10.9 Apr 6, 2014

Bioconductor support for R-3.1.0 on Mavericks (Mac OS X 10.9)

1 msg
Dan Tenenbaum Bioconductor support for R-3.1.0 on Mavericks (Mac OS X 10.9) Apr 4, 2014

Bug in as.data.frame method for RangedData?

2 msgs
Kevin Ushey Bug in as.data.frame method for RangedData? Apr 28, 2014 Valerie Obenchain Bug in as.data.frame method for RangedData? Apr 28, 2014

CITATION on the Bioc package landing page?

4 msgs
Wolfgang Huber CITATION on the Bioc package landing page? Apr 24, 2014 Vincent Carey CITATION on the Bioc package landing page? Apr 24, 2014 Michael Lawrence CITATION on the Bioc package landing page? Apr 24, 2014 Martin Morgan CITATION on the Bioc package landing page? Apr 25, 2014

Can\'t load new BioC packages

2 msgs
Nicolas Delhomme Can\'t load new BioC packages Apr 15, 2014 Dan Tenenbaum Can\'t load new BioC packages Apr 15, 2014

Commit Problem

2 msgs
Morganella Sandro Commit Problem Apr 9, 2014 Dan Du Commit Problem Apr 9, 2014

Conflicting definitions for function redefined as S4 generics

2 msgs
Ulrich Bodenhofer Conflicting definitions for function redefined as S4 generics Apr 3, 2014 Michael Lawrence Conflicting definitions for function redefined as S4 generics Apr 3, 2014

Dependency on windowing systems in the flowCore package

14 msgs
Kieran O'Neill Dependency on windowing systems in the flowCore package Apr 10, 2014 Dan Tenenbaum Dependency on windowing systems in the flowCore package Apr 10, 2014 Kieran O'Neill Dependency on windowing systems in the flowCore package Apr 10, 2014 Kevin Ushey Dependency on windowing systems in the flowCore package Apr 10, 2014 Kasper Daniel Hansen Dependency on windowing systems in the flowCore package Apr 10, 2014 Kevin Ushey Dependency on windowing systems in the flowCore package Apr 10, 2014 Kieran O'Neill Dependency on windowing systems in the flowCore package Apr 10, 2014 Mike Dependency on windowing systems in the flowCore package Apr 16, 2014 Mike Dependency on windowing systems in the flowCore package Apr 17, 2014 Martin Morgan Dependency on windowing systems in the flowCore package Apr 18, 2014 Mike Dependency on windowing systems in the flowCore package Apr 18, 2014 Kieran O'Neill Dependency on windowing systems in the flowCore package Apr 22, 2014 Mike Dependency on windowing systems in the flowCore package Apr 22, 2014 Josef Spidlen Dependency on windowing systems in the flowCore package Apr 23, 2014

Gviz AnnotationTrack ylim patch

1 msg
Lance Parsons Gviz AnnotationTrack ylim patch Apr 30, 2014

IRanges:::safeExplode

3 msgs
Tengfei Yin IRanges:::safeExplode Apr 23, 2014 Hervé Pagès IRanges:::safeExplode Apr 23, 2014 Tengfei Yin IRanges:::safeExplode Apr 24, 2014

Important: Bioconductor 2.14 branch to be created today

2 msgs
Dan Tenenbaum Important: Bioconductor 2.14 branch to be created today Apr 11, 2014 Dan Tenenbaum Important: Bioconductor 2.14 branch to be created today Apr 11, 2014

Lazy evaluation and S4 methods

5 msgs
Kevin Ushey Lazy evaluation and S4 methods Apr 23, 2014 Michael Lawrence Lazy evaluation and S4 methods Apr 23, 2014 Kevin Ushey Lazy evaluation and S4 methods Apr 23, 2014 Michael Lawrence Lazy evaluation and S4 methods Apr 23, 2014 Kevin Ushey Lazy evaluation and S4 methods Apr 23, 2014

Missing seqinfo method for BamFileList?

3 msgs
Ryan Missing seqinfo method for BamFileList? Apr 25, 2014 Martin Morgan Missing seqinfo method for BamFileList? Apr 25, 2014 Ryan Missing seqinfo method for BamFileList? Apr 26, 2014

New package version and BiocCheck

3 msgs
Dan Gatti New package version and BiocCheck Apr 18, 2014 Dan Tenenbaum New package version and BiocCheck Apr 18, 2014 Dan Tenenbaum New package version and BiocCheck Apr 18, 2014

No propagation from the GitHub bridge (clonotypeR package).

1 msg
Charles Plessy No propagation from the GitHub bridge (clonotypeR package). Apr 8, 2014

Old version of packages

3 msgs
Gustavo H. Esteves Old version of packages Apr 10, 2014 Dan Tenenbaum Old version of packages Apr 10, 2014 Gustavo H. Esteves Old version of packages Apr 10, 2014

Package vignette and knitr

3 msgs
Davide Risso Package vignette and knitr Apr 22, 2014 Dan Tenenbaum Package vignette and knitr Apr 22, 2014 Davide Risso Package vignette and knitr Apr 22, 2014

Packaging a medium/large project

4 msgs
ushi Packaging a medium/large project Apr 16, 2014 Julian Gehring Packaging a medium/large project Apr 16, 2014 Julian Gehring Packaging a medium/large project Apr 16, 2014 Gabriel Becker Packaging a medium/large project Apr 16, 2014

Preparing package release notes

1 msg
Dan Tenenbaum Preparing package release notes Apr 7, 2014

Restrictions on findOverlaps parameters with SummarizedExperiment objects

3 msgs
Peter Hickey Restrictions on findOverlaps parameters with SummarizedExperiment objects Apr 10, 2014 Martin Morgan Restrictions on findOverlaps parameters with SummarizedExperiment objects Apr 11, 2014 Peter Hickey Restrictions on findOverlaps parameters with SummarizedExperiment objects Apr 11, 2014

Rsamtools applyPileups function not merging positions from multiple files if not identical

6 msgs
Jonathon Hill Rsamtools applyPileups function not merging positions from multiple files if not identical Apr 21, 2014 Martin Morgan Rsamtools applyPileups function not merging positions from multiple files if not identical Apr 21, 2014 Jonathon Hill Rsamtools applyPileups function not merging positions from multiple files if not identical Apr 22, 2014 Martin Morgan Rsamtools applyPileups function not merging positions from multiple files if not identical Apr 23, 2014 Jonathon Hill Rsamtools applyPileups function not merging positions from multiple files if not identical Apr 29, 2014 Martin Morgan Rsamtools applyPileups function not merging positions from multiple files if not identical Apr 29, 2014

Rsamtools: Is extdata/ex1.bam.bai outdated?

3 msgs
Henrik Bengtsson Rsamtools: Is extdata/ex1.bam.bai outdated? Apr 18, 2014 Martin Morgan Rsamtools: Is extdata/ex1.bam.bai outdated? Apr 21, 2014 Henrik Bengtsson Rsamtools: Is extdata/ex1.bam.bai outdated? Apr 21, 2014

S4Vectors package

1 msg
Hervé Pagès S4Vectors package Apr 17, 2014

Subsetting Lists by Lists

13 msgs
Michael Lawrence Subsetting Lists by Lists Apr 1, 2014 Cook, Malcolm Subsetting Lists by Lists Apr 1, 2014 Ryan Subsetting Lists by Lists Apr 1, 2014 Tim Triche, Jr. Subsetting Lists by Lists Apr 1, 2014 Hervé Pagès Subsetting Lists by Lists Apr 1, 2014 Hervé Pagès Subsetting Lists by Lists Apr 1, 2014 Michael Lawrence Subsetting Lists by Lists Apr 1, 2014 Hervé Pagès Subsetting Lists by Lists Apr 1, 2014 Hervé Pagès Subsetting Lists by Lists Apr 1, 2014 Hervé Pagès Subsetting Lists by Lists Apr 1, 2014 Tim Triche, Jr. Subsetting Lists by Lists Apr 1, 2014 Michael Lawrence Subsetting Lists by Lists Apr 1, 2014 Hervé Pagès Subsetting Lists by Lists Apr 3, 2014

beadarray warning (seqlevelsStyle?)

4 msgs
Mark Dunning beadarray warning (seqlevelsStyle?) Apr 1, 2014 Martin Rijlaarsdam beadarray warning (seqlevelsStyle?) Apr 1, 2014 Arora, Sonali beadarray warning (seqlevelsStyle?) Apr 1, 2014 Arora, Sonali beadarray warning (seqlevelsStyle?) Apr 1, 2014

biocLite “no packages in repository” error

5 msgs
Dan Tenenbaum biocLite “no packages in repository” error Apr 15, 2014 Dan Tenenbaum biocLite “no packages in repository” error Apr 15, 2014 Nicolas Delhomme biocLite “no packages in repository” error Apr 15, 2014 Dan Tenenbaum biocLite “no packages in repository” error Apr 15, 2014 Nicolas Delhomme biocLite “no packages in repository” error Apr 15, 2014

compare generics

3 msgs
Laurent Gatto compare generics Apr 9, 2014 Hervé Pagès compare generics Apr 10, 2014 Laurent Gatto compare generics Apr 11, 2014

error in summary method for KEGGHyperGResult

3 msgs
Gabriel Becker error in summary method for KEGGHyperGResult Apr 24, 2014 James W. MacDonald error in summary method for KEGGHyperGResult Apr 24, 2014 Gabriel Becker error in summary method for KEGGHyperGResult Apr 24, 2014

git svn bridge is broken

2 msgs
Mike git svn bridge is broken Apr 24, 2014 Dan Tenenbaum git svn bridge is broken Apr 24, 2014

git-svn bridge down?

11 msgs
Julian Gehring git-svn bridge down? Apr 7, 2014 Dan Tenenbaum git-svn bridge down? Apr 7, 2014 Julian Gehring git-svn bridge down? Apr 7, 2014 Dan Tenenbaum git-svn bridge down? Apr 7, 2014 Julian Gehring git-svn bridge down? Apr 8, 2014 Julian Gehring git-svn bridge down? Apr 8, 2014 Neumann, Steffen git-svn bridge down? Apr 8, 2014 Dan Tenenbaum git-svn bridge down? Apr 8, 2014 Dan Tenenbaum git-svn bridge down? Apr 8, 2014 Dan Tenenbaum git-svn bridge down? Apr 8, 2014 Dan Tenenbaum git-svn bridge down? Apr 8, 2014

metadata() in BiocGenerics?

5 msgs
Vincent Carey metadata() in BiocGenerics? Apr 10, 2014 Hervé Pagès metadata() in BiocGenerics? Apr 16, 2014 Vincent Carey metadata() in BiocGenerics? Apr 17, 2014 Michael Lawrence metadata() in BiocGenerics? Apr 17, 2014 Hervé Pagès metadata() in BiocGenerics? Apr 22, 2014

preservation of names by translate,DNAStringSet

2 msgs
Michael Lawrence preservation of names by translate,DNAStringSet Apr 3, 2014 Hervé Pagès preservation of names by translate,DNAStringSet Apr 3, 2014

r+w permissions in release branches

18 msgs
Alejandro Reyes r+w permissions in release branches Apr 22, 2014 Kasper Daniel Hansen r+w permissions in release branches Apr 22, 2014 Andrzej Oleś r+w permissions in release branches Apr 22, 2014 Alejandro Reyes r+w permissions in release branches Apr 22, 2014 Julian Gehring r+w permissions in release branches Apr 22, 2014 Wolfgang Huber r+w permissions in release branches Apr 22, 2014 Julian Gehring r+w permissions in release branches Apr 22, 2014 Kasper Daniel Hansen r+w permissions in release branches Apr 22, 2014 Martin Morgan r+w permissions in release branches Apr 23, 2014 Wolfgang Huber r+w permissions in release branches Apr 24, 2014 Kasper Daniel Hansen r+w permissions in release branches Apr 24, 2014 Wolfgang Huber r+w permissions in release branches Apr 24, 2014 Steve Lianoglou r+w permissions in release branches Apr 24, 2014 Hervé Pagès r+w permissions in release branches Apr 25, 2014 Kasper Daniel Hansen r+w permissions in release branches Apr 30, 2014 Martin Morgan r+w permissions in release branches Apr 30, 2014 Kasper Daniel Hansen r+w permissions in release branches Apr 30, 2014 Michael Lawrence r+w permissions in release branches Apr 30, 2014

rbind,DataFrame vs rbind.data.frame

3 msgs
Hervé Pagès rbind,DataFrame vs rbind.data.frame Apr 29, 2014 Michael Lawrence rbind,DataFrame vs rbind.data.frame Apr 30, 2014 Hervé Pagès rbind,DataFrame vs rbind.data.frame Apr 30, 2014

renameSeqlevels name matching

3 msgs
Michael Lawrence renameSeqlevels name matching Apr 3, 2014 Arora, Sonali renameSeqlevels name matching Apr 3, 2014 Michael Lawrence renameSeqlevels name matching Apr 3, 2014

restrictToSNV for VCF

1 msg
Valerie Obenchain restrictToSNV for VCF Apr 9, 2014

rownames in SummerizedExperiments

9 msgs
Simon Anders rownames in SummerizedExperiments Apr 5, 2014 Simon Anders rownames in SummerizedExperiments Apr 5, 2014 Michael Lawrence rownames in SummerizedExperiments Apr 6, 2014 Simon Anders rownames in SummerizedExperiments Apr 6, 2014 Michael Lawrence rownames in SummerizedExperiments Apr 6, 2014 Martin Morgan rownames in SummerizedExperiments Apr 6, 2014 Michael Lawrence rownames in SummerizedExperiments Apr 6, 2014 Simon Anders rownames in SummerizedExperiments Apr 6, 2014 Hervé Pagès rownames in SummerizedExperiments Apr 6, 2014

seqlevelsStyle<- doesn't work for GRanges object

4 msgs
Tengfei Yin seqlevelsStyle<- doesn't work for GRanges object Apr 10, 2014 Tengfei Yin seqlevelsStyle<- doesn't work for GRanges object Apr 10, 2014 Hervé Pagès seqlevelsStyle<- doesn't work for GRanges object Apr 11, 2014 Tengfei Yin seqlevelsStyle<- doesn't work for GRanges object Apr 11, 2014

strange spam from biocbuild

1 msg
Marc Carlson strange spam from biocbuild Apr 17, 2014

suggestion about bioconductor package-- BSgenome.Hsapiens.NCBI.GRCh38

4 msgs
Hervé Pagès suggestion about bioconductor package-- BSgenome.Hsapiens.NCBI.GRCh38 Apr 16, 2014 Michael Lawrence suggestion about bioconductor package-- BSgenome.Hsapiens.NCBI.GRCh38 Apr 16, 2014 Hervé Pagès suggestion about bioconductor package-- BSgenome.Hsapiens.NCBI.GRCh38 Apr 16, 2014 Michael Lawrence suggestion about bioconductor package-- BSgenome.Hsapiens.NCBI.GRCh38 Apr 16, 2014

suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38

7 msgs
Michael Lawrence suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38 Apr 20, 2014 Hervé Pagès suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38 Apr 20, 2014 Martin Morgan suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38 Apr 20, 2014 Martin Morgan suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38 Apr 20, 2014 Tim Triche, Jr. suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38 Apr 20, 2014 Hervé Pagès suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38 Apr 20, 2014 Tim Triche, Jr. suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38 Apr 20, 2014

svn repository for data experiment packages now having branches too

2 msgs
Laurent Gatto svn repository for data experiment packages now having branches too Apr 1, 2014 Bernd Fischer svn repository for data experiment packages now having branches too Apr 1, 2014

unexpected build and check error

5 msgs
Luo Weijun unexpected build and check error Apr 4, 2014 Martin Morgan unexpected build and check error Apr 5, 2014 Luo Weijun unexpected build and check error Apr 6, 2014 Dan Tenenbaum unexpected build and check error Apr 6, 2014 Luo Weijun unexpected build and check error Apr 7, 2014