Bioc-devel May 2014

[Bioc-devel] viewMedians

2 msgs May 30

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Michael Lawrence viewMedians May 30, 2014

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Hervé Pagès viewMedians May 30, 2014

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

4 msgs May 30

M

Martin Morgan CITATION on the Bioc package landing page? May 30, 2014

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Vincent Carey CITATION on the Bioc package landing page? May 30, 2014

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Michael Lawrence CITATION on the Bioc package landing page? May 30, 2014

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Vincent Carey CITATION on the Bioc package landing page? May 30, 2014

[Bioc-devel] BiocCheck

4 msgs May 29

D

Dan Tenenbaum BiocCheck May 29, 2014

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Kasper Daniel Hansen BiocCheck May 29, 2014

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Dan Tenenbaum BiocCheck May 29, 2014

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Kasper Daniel Hansen BiocCheck May 29, 2014

[Bioc-devel] Bioc 2014: reduced hotel rates

1 msg May 29

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Martin Morgan Bioc 2014: reduced hotel rates May 29, 2014

[Bioc-devel] My "==" method breaks existing "==" method for signature c("Rle", "vector')

5 msgs May 28

P

Peter Hickey My "==" method breaks existing "==" method for signature c("Rle", "vector') May 25, 2014

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Martin Morgan My "==" method breaks existing "==" method for signature c("Rle", "vector') May 26, 2014

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Peter Hickey My "==" method breaks existing "==" method for signature c("Rle", "vector') May 26, 2014

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Hervé Pagès My "==" method breaks existing "==" method for signature c("Rle", "vector') May 27, 2014

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Peter Hickey My "==" method breaks existing "==" method for signature c("Rle", "vector') May 28, 2014

[Bioc-devel] BiocCheck

1 msg May 28

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Kasper Daniel Hansen BiocCheck May 28, 2014

[Bioc-devel] Bug tracker for Bioconductor?

20 msgs May 27

K

Keith Hughitt Bug tracker for Bioconductor? May 20, 2014

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Nicolas Delhomme Bug tracker for Bioconductor? May 20, 2014

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Keith Hughitt Bug tracker for Bioconductor? May 23, 2014

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Cook, Malcolm Bug tracker for Bioconductor? May 23, 2014

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Michael Lawrence Bug tracker for Bioconductor? May 23, 2014

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Cook, Malcolm Bug tracker for Bioconductor? May 23, 2014

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Kasper Daniel Hansen Bug tracker for Bioconductor? May 23, 2014

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Michael Lawrence Bug tracker for Bioconductor? May 23, 2014

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Dan Tenenbaum Bug tracker for Bioconductor? May 23, 2014

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Michael Lawrence Bug tracker for Bioconductor? May 23, 2014

Y

Yihui Xie Bug tracker for Bioconductor? May 23, 2014

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Vincent Carey Bug tracker for Bioconductor? May 23, 2014

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Michael Lawrence Bug tracker for Bioconductor? May 23, 2014

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Sean Davis Bug tracker for Bioconductor? May 23, 2014

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Michael Lawrence Bug tracker for Bioconductor? May 23, 2014

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Martin Morgan Bug tracker for Bioconductor? May 24, 2014

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Martin Morgan Bug tracker for Bioconductor? May 24, 2014

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Aniba, Radhouane Bug tracker for Bioconductor? May 24, 2014

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Cook, Malcolm Bug tracker for Bioconductor? May 27, 2014

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Cook, Malcolm Bug tracker for Bioconductor? May 27, 2014

[Bioc-devel] can't create git-svn bridge

2 msgs May 26

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Doug H. Phanstiel can't create git-svn bridge May 26, 2014

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Dan Tenenbaum can't create git-svn bridge May 26, 2014

[Bioc-devel] Bioconductor git-svn bridge is available

11 msgs May 23

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Moritz Gerstung Bioconductor git-svn bridge is available May 12, 2014

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Dan Tenenbaum Bioconductor git-svn bridge is available May 12, 2014

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Henrik Bengtsson Bioconductor git-svn bridge is available May 12, 2014

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Dan Tenenbaum Bioconductor git-svn bridge is available May 12, 2014

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Hector Corrada Bravo Bioconductor git-svn bridge is available May 12, 2014

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Kasper Daniel Hansen Bioconductor git-svn bridge is available May 21, 2014

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Dan Tenenbaum Bioconductor git-svn bridge is available May 21, 2014

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Kasper Daniel Hansen Bioconductor git-svn bridge is available May 21, 2014

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Dan Tenenbaum Bioconductor git-svn bridge is available May 21, 2014

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Ilari Scheinin Bioconductor git-svn bridge is available May 23, 2014

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Dan Tenenbaum Bioconductor git-svn bridge is available May 23, 2014

[Bioc-devel] "nearest" & related methods for GRangesList & friends?

4 msgs May 23

R

Ryan "nearest" & related methods for GRangesList & friends? May 22, 2014

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Hervé Pagès "nearest" & related methods for GRangesList & friends? May 23, 2014

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Ryan "nearest" & related methods for GRangesList & friends? May 23, 2014

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Hervé Pagès "nearest" & related methods for GRangesList & friends? May 23, 2014

[Bioc-devel] Namespace issues with ggbio 1.13.6 from AnnotationDbi 1.27.6 not exporting 'cols'

5 msgs May 23

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Leonardo Collado Torres Namespace issues with ggbio 1.13.6 from AnnotationDbi 1.27.6 not exporting 'cols' May 22, 2014

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Tengfei Yin Namespace issues with ggbio 1.13.6 from AnnotationDbi 1.27.6 not exporting 'cols' May 22, 2014

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Dan Tenenbaum Namespace issues with ggbio 1.13.6 from AnnotationDbi 1.27.6 not exporting 'cols' May 22, 2014

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Tengfei Yin Namespace issues with ggbio 1.13.6 from AnnotationDbi 1.27.6 not exporting 'cols' May 22, 2014

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Leonardo Collado Torres Namespace issues with ggbio 1.13.6 from AnnotationDbi 1.27.6 not exporting 'cols' May 23, 2014

[Bioc-devel] bioconductor AMI & shiny app

4 msgs May 22

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Robert Castelo bioconductor AMI & shiny app May 21, 2014

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Dan Tenenbaum bioconductor AMI & shiny app May 21, 2014

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Robert Castelo bioconductor AMI & shiny app May 22, 2014

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Dan Tenenbaum bioconductor AMI & shiny app May 22, 2014

[Bioc-devel] GenomicRanges: Concatenation of GRanges with matrices in mcols

4 msgs May 20

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Julian Gehring GenomicRanges: Concatenation of GRanges with matrices in mcols May 20, 2014

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Hervé Pagès GenomicRanges: Concatenation of GRanges with matrices in mcols May 20, 2014

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Hervé Pagès GenomicRanges: Concatenation of GRanges with matrices in mcols May 20, 2014

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Michael Lawrence GenomicRanges: Concatenation of GRanges with matrices in mcols May 20, 2014

[Bioc-devel] Slow performance on scanBam

5 msgs May 20

J

James Bullard Slow performance on scanBam May 12, 2014

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Martin Morgan Slow performance on scanBam May 13, 2014

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James Bullard Slow performance on scanBam May 13, 2014

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Martin Morgan Slow performance on scanBam May 20, 2014

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James Bullard Slow performance on scanBam May 20, 2014

[Bioc-devel] Contradictory Clinical Data in curatedOvarianData

2 msgs May 20

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Dario Strbenac Contradictory Clinical Data in curatedOvarianData May 20, 2014

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Topsoil Wang Contradictory Clinical Data in curatedOvarianData May 20, 2014

[Bioc-devel] git-svn bridge: Track devel and release in different branches of same repo

4 msgs May 19

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Julian Gehring git-svn bridge: Track devel and release in different branches of same repo May 14, 2014

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Ilari Scheinin git-svn bridge: Track devel and release in different branches of same repo May 15, 2014

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Robert M. Flight git-svn bridge: Track devel and release in different branches of same repo May 15, 2014

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Julian Gehring git-svn bridge: Track devel and release in different branches of same repo May 19, 2014

[Bioc-devel] extracting low-level stuff from Biobase

4 msgs May 16

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Michael Lawrence extracting low-level stuff from Biobase May 16, 2014

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Vincent Carey extracting low-level stuff from Biobase May 16, 2014

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Kasper Daniel Hansen extracting low-level stuff from Biobase May 16, 2014

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Michael Lawrence extracting low-level stuff from Biobase May 16, 2014

[Bioc-devel] git-svn bridge: Track devel and release in different branches of same repo

1 msg May 14

D

Dan Tenenbaum git-svn bridge: Track devel and release in different branches of same repo May 14, 2014

[Bioc-devel] new 2bit BSgenome data packages

1 msg May 13

H

Hervé Pagès new 2bit BSgenome data packages May 13, 2014

[Bioc-devel] R CMD CHECK options

5 msgs May 13

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Siddhartha Bagaria R CMD CHECK options May 12, 2014

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Dan Tenenbaum R CMD CHECK options May 12, 2014

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Siddhartha Bagaria R CMD CHECK options May 13, 2014

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Dan Tenenbaum R CMD CHECK options May 13, 2014

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Gabriel Becker R CMD CHECK options May 13, 2014

[Bioc-devel] [BioC] granges() method for GenomicRanges objects akin to ranges()...

16 msgs May 13

T

Tim Triche, Jr. granges() method for GenomicRanges objects akin to ranges()... May 4, 2014

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Michael Lawrence granges() method for GenomicRanges objects akin to ranges()... May 4, 2014

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Julian Gehring granges() method for GenomicRanges objects akin to ranges()... May 5, 2014

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Tim Triche, Jr. granges() method for GenomicRanges objects akin to ranges()... May 5, 2014

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Michael Lawrence granges() method for GenomicRanges objects akin to ranges()... May 5, 2014

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Martin Morgan granges() method for GenomicRanges objects akin to ranges()... May 5, 2014

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Julian Gehring granges() method for GenomicRanges objects akin to ranges()... May 5, 2014

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Tim Triche, Jr. granges() method for GenomicRanges objects akin to ranges()... May 5, 2014

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Michael Lawrence granges() method for GenomicRanges objects akin to ranges()... May 5, 2014

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Kasper Daniel Hansen granges() method for GenomicRanges objects akin to ranges()... May 5, 2014

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Hervé Pagès granges() method for GenomicRanges objects akin to ranges()... May 5, 2014

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Cook, Malcolm granges() method for GenomicRanges objects akin to ranges()... May 5, 2014

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Hervé Pagès granges() method for GenomicRanges objects akin to ranges()... May 5, 2014

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Cook, Malcolm granges() method for GenomicRanges objects akin to ranges()... May 5, 2014

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Hervé Pagès granges() method for GenomicRanges objects akin to ranges()... May 5, 2014

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Julian Gehring granges() method for GenomicRanges objects akin to ranges()... May 13, 2014

[Bioc-devel] libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20

4 msgs May 12

E

E N libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20 May 6, 2014

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Martin Morgan libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20 May 6, 2014

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M. Edward (Ed) Borasky libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20 May 12, 2014

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M. Edward (Ed) Borasky libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20 May 12, 2014

[Bioc-devel] export() to 2bit file

5 msgs May 12

H

Hervé Pagès export() to 2bit file May 9, 2014

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Michael Lawrence export() to 2bit file May 9, 2014

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Hervé Pagès export() to 2bit file May 12, 2014

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Michael Lawrence export() to 2bit file May 12, 2014

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Hervé Pagès export() to 2bit file May 12, 2014

[Bioc-devel] larger BioC AMI EBS volume

4 msgs May 9

R

Robert Castelo larger BioC AMI EBS volume May 9, 2014

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Vincent Carey larger BioC AMI EBS volume May 9, 2014

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Dan Tenenbaum larger BioC AMI EBS volume May 9, 2014

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Robert Castelo larger BioC AMI EBS volume May 9, 2014

[Bioc-devel] error when creating gitsvn bridge

2 msgs May 9

J

Jonathon Hill error when creating gitsvn bridge May 9, 2014

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Dan Tenenbaum error when creating gitsvn bridge May 9, 2014

[Bioc-devel] deprecating GenomeData and GenomeDataList

6 msgs May 8

H

Hervé Pagès deprecating GenomeData and GenomeDataList May 8, 2014

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Michael Lawrence deprecating GenomeData and GenomeDataList May 8, 2014

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Hervé Pagès deprecating GenomeData and GenomeDataList May 8, 2014

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Dario Strbenac deprecating GenomeData and GenomeDataList May 8, 2014

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Hervé Pagès deprecating GenomeData and GenomeDataList May 8, 2014

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Michael Lawrence deprecating GenomeData and GenomeDataList May 8, 2014

[Bioc-devel] Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14)

6 msgs May 8

D

Don Armstrong Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14) May 7, 2014

M

Martin Morgan Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14) May 7, 2014

D

Dan Tenenbaum Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14) May 7, 2014

S

Steve Lianoglou Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14) May 8, 2014

D

Don Armstrong Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14) May 8, 2014

D

Dan Tenenbaum Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14) May 8, 2014

[Bioc-devel] names, mcols and metadata are not changed in "[<-" operator of class Vector

2 msgs May 7

H

Hervé Pagès names, mcols and metadata are not changed in "[<-" operator of class Vector May 7, 2014

S

Sebastian Gibb names, mcols and metadata are not changed in "[<-" operator of class Vector May 7, 2014

[Bioc-devel] change names(assays(SummarizedExperiment)) w/o copy?

2 msgs May 7

M

Michael Love change names(assays(SummarizedExperiment)) w/o copy? May 7, 2014

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Martin Morgan change names(assays(SummarizedExperiment)) w/o copy? May 7, 2014

[Bioc-devel] names, mcols and metadata are not changed in "[<-" operator of class Vector

1 msg May 7

S

Sebastian Gibb names, mcols and metadata are not changed in "[<-" operator of class Vector May 7, 2014

[Bioc-devel] libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20

6 msgs May 6

E

E N libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20 May 6, 2014

M

Martin Morgan libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20 May 6, 2014

E

E N libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20 May 6, 2014

E

E N libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20 May 6, 2014

M

Martin Morgan libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20 May 6, 2014

E

E N libRblas and libRlapack are broken dependencies for packages in R 3.1.0 on Fedora 20 May 6, 2014

[Bioc-devel] Question about which new organism resources to create

2 msgs May 6

M

Marc Carlson Question about which new organism resources to create May 6, 2014

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Luo Weijun Question about which new organism resources to create May 6, 2014

[Bioc-devel] [BioC] Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14

2 msgs May 6

D

Dan Tenenbaum Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14 May 6, 2014

D

Dan Tenenbaum Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14 May 6, 2014

[Bioc-devel] Is roxygen2 version 4.0.0 supported on the devel build system?

4 msgs May 6

N

Nicolas Delhomme Is roxygen2 version 4.0.0 supported on the devel build system? May 6, 2014

D

Dan Tenenbaum Is roxygen2 version 4.0.0 supported on the devel build system? May 6, 2014

D

Dan Tenenbaum Is roxygen2 version 4.0.0 supported on the devel build system? May 6, 2014

N

Nicolas Delhomme Is roxygen2 version 4.0.0 supported on the devel build system? May 6, 2014

[Bioc-devel] Gviz AnnotationTrack fails when "["-operator is defined

6 msgs May 6

S

Sebastian Gibb Gviz AnnotationTrack fails when "["-operator is defined May 4, 2014

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Hahne, Florian Gviz AnnotationTrack fails when "["-operator is defined May 5, 2014

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Sebastian Gibb Gviz AnnotationTrack fails when "["-operator is defined May 5, 2014

M

Martin Morgan Gviz AnnotationTrack fails when "["-operator is defined May 5, 2014

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Hahne, Florian Gviz AnnotationTrack fails when "["-operator is defined May 6, 2014

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Martin Morgan Gviz AnnotationTrack fails when "["-operator is defined May 6, 2014

[Bioc-devel] Gviz doesn't provide enough horizontial space

1 msg May 6

H

Hahne, Florian Gviz doesn't provide enough horizontial space May 6, 2014

[Bioc-devel] Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14

1 msg May 5

D

Dan Tenenbaum Mavericks (Mac OS X 10.9) binary Bioconductor packages available for BioC 2.14 May 5, 2014

[Bioc-devel] Gviz AnnotationTrack ylim patch

1 msg May 5

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Hahne, Florian Gviz AnnotationTrack ylim patch May 5, 2014

[Bioc-devel] Gviz doesn't provide enough horizontial space

2 msgs May 5

S

Sebastian Gibb Gviz doesn't provide enough horizontial space May 2, 2014

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Hahne, Florian Gviz doesn't provide enough horizontial space May 5, 2014

[Bioc-devel] Installing Annotation Packages Matching a Pattern

5 msgs May 5

D

Dario Strbenac Installing Annotation Packages Matching a Pattern May 4, 2014

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Martin Morgan Installing Annotation Packages Matching a Pattern May 4, 2014

H

Hervé Pagès Installing Annotation Packages Matching a Pattern May 4, 2014

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Dario Strbenac Installing Annotation Packages Matching a Pattern May 4, 2014

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Kasper Daniel Hansen Installing Annotation Packages Matching a Pattern May 5, 2014

[Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...

1 msg May 4

T

Tim Triche, Jr. granges() method for GenomicRanges objects akin to ranges()... May 4, 2014

[Bioc-devel] Convertion of DataFrame with XStringSets to data.frame

3 msgs May 2

J

Julian Gehring Convertion of DataFrame with XStringSets to data.frame May 2, 2014

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Michael Lawrence Convertion of DataFrame with XStringSets to data.frame May 2, 2014

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Hervé Pagès Convertion of DataFrame with XStringSets to data.frame May 2, 2014

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

4 msgs May 1

V

Valerie Obenchain Additional summarizeOverlaps counting modes for ChIP-Seq May 1, 2014

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Ryan Additional summarizeOverlaps counting modes for ChIP-Seq May 1, 2014

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Valerie Obenchain Additional summarizeOverlaps counting modes for ChIP-Seq May 1, 2014

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Valerie Obenchain Additional summarizeOverlaps counting modes for ChIP-Seq May 1, 2014

[Bioc-devel] BioC 2014 Registration Open

1 msg May 1

M

Martin Morgan BioC 2014 Registration Open May 1, 2014

[Bioc-devel] Gviz AlignmentTrack ylim patch

1 msg May 1

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Lance Parsons Gviz AlignmentTrack ylim patch May 1, 2014