Bioc-devel - April 2014 - Thread View

[Bioc-devel] r+w permissions in release branches

18 msgs Apr 30

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

[Bioc-devel] Additional summarizeOverlaps counting modes for ChIP-Seq

3 msgs Apr 30

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

[Bioc-devel] Gviz AnnotationTrack ylim patch

1 msg Apr 30

Lance Parsons Gviz AnnotationTrack ylim patch Apr 30, 2014

[Bioc-devel] rbind,DataFrame vs rbind.data.frame

3 msgs Apr 30

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

[Bioc-devel] Rsamtools applyPileups function not merging positions from multiple files if not identical

2 msgs Apr 29

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

[Bioc-devel] Bug in as.data.frame method for RangedData?

1 msg Apr 28

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

[Bioc-devel] Bug in as.data.frame method for RangedData?

1 msg Apr 28

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

[Bioc-devel] Missing seqinfo method for BamFileList?

2 msgs Apr 26

Martin Morgan Missing seqinfo method for BamFileList? Apr 25, 2014

Ryan Missing seqinfo method for BamFileList? Apr 26, 2014

[Bioc-devel] Missing seqinfo method for BamFileList?

1 msg Apr 25

Ryan Missing seqinfo method for BamFileList? Apr 25, 2014

[Bioc-devel] CITATION on the Bioc package landing page?

4 msgs Apr 25

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

[Bioc-devel] New package version and BiocCheck

3 msgs Apr 25

Dan Tenenbaum New package version and BiocCheck Apr 18, 2014

Michael Stadler 'memory not mapped' in trimLRpatterns Apr 22, 2014

Hervé Pagès 'memory not mapped' in trimLRpatterns Apr 25, 2014

[Bioc-devel] git svn bridge is broken

2 msgs Apr 24

Mike git svn bridge is broken Apr 24, 2014

Dan Tenenbaum git svn bridge is broken Apr 24, 2014

[Bioc-devel] IRanges:::safeExplode

2 msgs Apr 24

Hervé Pagès IRanges:::safeExplode Apr 23, 2014

Tengfei Yin IRanges:::safeExplode Apr 24, 2014

[Bioc-devel] error in summary method for KEGGHyperGResult

3 msgs Apr 24

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

[Bioc-devel] Dependency on windowing systems in the flowCore package

1 msg Apr 23

Josef Spidlen Dependency on windowing systems in the flowCore package Apr 23, 2014

[Bioc-devel] IRanges:::safeExplode

1 msg Apr 23

Tengfei Yin IRanges:::safeExplode Apr 23, 2014

[Bioc-devel] Lazy evaluation and S4 methods

5 msgs Apr 23

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

[Bioc-devel] Rsamtools applyPileups function not merging positions from multiple files if not identical

4 msgs Apr 23

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

[Bioc-devel] metadata() in BiocGenerics?

5 msgs Apr 22

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

[Bioc-devel] Package vignette and knitr

3 msgs Apr 22

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

[Bioc-devel] Dependency on windowing systems in the flowCore package

4 msgs Apr 22

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

[Bioc-devel] BiocUpgrades updates to devel instead of stable

5 msgs Apr 22

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

Martin Morgan BiocUpgrades updates to devel instead of stable Apr 22, 2014

[Bioc-devel] Rsamtools: Is extdata/ex1.bam.bai outdated?

3 msgs Apr 21

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

[Bioc-devel] Fwd: Re: [devteam-bioc] suggestion about bioconductorpackage-- BSgenome.Hsapiens.NCBI.GRCh38

7 msgs Apr 20

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

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

[Bioc-devel] New package version and BiocCheck

2 msgs Apr 18

Dan Gatti New package version and BiocCheck Apr 18, 2014

Dan Tenenbaum New package version and BiocCheck Apr 18, 2014

[Bioc-devel] Dependency on windowing systems in the flowCore package

2 msgs Apr 17

Mike Dependency on windowing systems in the flowCore package Apr 16, 2014

Mike Dependency on windowing systems in the flowCore package Apr 17, 2014

[Bioc-devel] strange spam from biocbuild

1 msg Apr 17

Marc Carlson strange spam from biocbuild Apr 17, 2014

[Bioc-devel] Apparent error in illuminaHumanv4.db

1 msg Apr 17

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

[Bioc-devel] S4Vectors package

1 msg Apr 17

Hervé Pagès S4Vectors package Apr 17, 2014

[Bioc-devel] [devteam-bioc] suggestion about bioconductor package-- BSgenome.Hsapiens.NCBI.GRCh38

4 msgs Apr 16

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

[Bioc-devel] Packaging a medium/large project

2 msgs Apr 16

Julian Gehring Packaging a medium/large project Apr 16, 2014

Gabriel Becker Packaging a medium/large project Apr 16, 2014

[Bioc-devel] Packaging a medium/large project

2 msgs Apr 16

ushi Packaging a medium/large project Apr 16, 2014

Julian Gehring Packaging a medium/large project Apr 16, 2014

[Bioc-devel] [BioC] Can\'t load new BioC packages

2 msgs Apr 15

Nicolas Delhomme Can\'t load new BioC packages Apr 15, 2014

Dan Tenenbaum Can\'t load new BioC packages Apr 15, 2014

[Bioc-devel] biocLite “no packages in repository” error

5 msgs Apr 15

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

[Bioc-devel] Bioconductor 2.14 is released

1 msg Apr 14

Dan Tenenbaum Bioconductor 2.14 is released Apr 14, 2014

[Bioc-devel] Restrictions on findOverlaps parameters with SummarizedExperiment objects

2 msgs Apr 11

Martin Morgan Restrictions on findOverlaps parameters with SummarizedExperiment objects Apr 11, 2014

Peter Hickey Restrictions on findOverlaps parameters with SummarizedExperiment objects Apr 11, 2014

[Bioc-devel] BioC 2.14 branch created

1 msg Apr 11

Dan Tenenbaum BioC 2.14 branch created Apr 11, 2014

[Bioc-devel] Important: Bioconductor 2.14 branch to be created today

2 msgs Apr 11

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

[Bioc-devel] seqlevelsStyle<- doesn't work for GRanges object

2 msgs Apr 11

Hervé Pagès seqlevelsStyle<- doesn't work for GRanges object Apr 11, 2014

Tengfei Yin seqlevelsStyle<- doesn't work for GRanges object Apr 11, 2014

[Bioc-devel] compare generics

2 msgs Apr 11

Hervé Pagès compare generics Apr 10, 2014

Laurent Gatto compare generics Apr 11, 2014

[Bioc-devel] Restrictions on findOverlaps parameters with SummarizedExperiment objects

1 msg Apr 10

Peter Hickey Restrictions on findOverlaps parameters with SummarizedExperiment objects Apr 10, 2014

[Bioc-devel] Dependency on windowing systems in the flowCore package

7 msgs Apr 10

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

[Bioc-devel] seqlevelsStyle<- doesn't work for GRanges object

2 msgs Apr 10

Tengfei Yin seqlevelsStyle<- doesn't work for GRanges object Apr 10, 2014

[Bioc-devel] Old version of packages

3 msgs Apr 10

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

[Bioc-devel] "[[<-" method dispatch and GenomicRanges

4 msgs Apr 9

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

[Bioc-devel] compare generics

1 msg Apr 9

Laurent Gatto compare generics Apr 9, 2014

[Bioc-devel] restrictToSNV for VCF

1 msg Apr 9

Valerie Obenchain restrictToSNV for VCF Apr 9, 2014

[Bioc-devel] Commit Problem

2 msgs Apr 9

Morganella Sandro Commit Problem Apr 9, 2014

Dan Du Commit Problem Apr 9, 2014

[Bioc-devel] git-svn bridge down?

11 msgs Apr 8

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

Neumann, Steffen git-svn bridge down? Apr 8, 2014

Dan Tenenbaum git-svn bridge down? Apr 8, 2014

[Bioc-devel] No propagation from the GitHub bridge (clonotypeR package).

1 msg Apr 8

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

[Bioc-devel] unexpected build and check error

5 msgs Apr 7

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

[Bioc-devel] Preparing package release notes

1 msg Apr 7

Dan Tenenbaum Preparing package release notes Apr 7, 2014

[Bioc-devel] rownames in SummerizedExperiments

9 msgs Apr 6

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

[Bioc-devel] Bioconductor packages for R-3.1.0 beta on OSX 10.9

4 msgs Apr 6

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

[Bioc-devel] Bioconductor support for R-3.1.0 on Mavericks (Mac OS X 10.9)

1 msg Apr 4

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

[Bioc-devel] A question on IRanges package

11 msgs Apr 4

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

Gabriel Becker A question on IRanges package Apr 3, 2014

Martin Morgan A question on IRanges package Apr 4, 2014

[Bioc-devel] Subsetting Lists by Lists

12 msgs Apr 3

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

Michael Lawrence 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

[Bioc-devel] preservation of names by translate,DNAStringSet

2 msgs Apr 3

Michael Lawrence preservation of names by translate,DNAStringSet Apr 3, 2014

Hervé Pagès preservation of names by translate,DNAStringSet Apr 3, 2014

[Bioc-devel] renameSeqlevels name matching

2 msgs Apr 3

Arora, Sonali renameSeqlevels name matching Apr 3, 2014

Michael Lawrence renameSeqlevels name matching Apr 3, 2014

[Bioc-devel] renameSeqlevels name matching

1 msg Apr 3

Michael Lawrence renameSeqlevels name matching Apr 3, 2014

[Bioc-devel] [Rd] Conflicting definitions for function redefined as S4 generics

2 msgs Apr 3

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

[Bioc-devel] Subsetting Lists by Lists

1 msg Apr 1

Hervé Pagès Subsetting Lists by Lists Apr 1, 2014

[Bioc-devel] beadarray warning (seqlevelsStyle?)

3 msgs Apr 1

Mark Dunning beadarray warning (seqlevelsStyle?) Apr 1, 2014

Martin Rijlaarsdam beadarray warning (seqlevelsStyle?) Apr 1, 2014

Arora, Sonali beadarray warning (seqlevelsStyle?) Apr 1, 2014

[Bioc-devel] beadarray warning (seqlevelsStyle?)

1 msg Apr 1

Arora, Sonali beadarray warning (seqlevelsStyle?) Apr 1, 2014

[Bioc-devel] BiocCheck: Allowed formats for vignette source

2 msgs Apr 1

Julian Gehring BiocCheck: Allowed formats for vignette source Apr 1, 2014

Dan Tenenbaum BiocCheck: Allowed formats for vignette source Apr 1, 2014

[Bioc-devel] Bioconductor newsletter: April 2014

3 msgs Apr 1

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

[Bioc-devel] svn repository for data experiment packages now having branches too

2 msgs Apr 1

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

Bioc-devel April 2014