Bioc-devel September 2014

[Bioc-devel] Cannot interact with a BigWig file on the web with rtracklayer (Windows specific)

2 msgs Sep 30

V

Valerie Obenchain Cannot interact with a BigWig file on the web with rtracklayer (Windows specific) Sep 30, 2014

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Leonardo Collado Torres Cannot interact with a BigWig file on the web with rtracklayer (Windows specific) Sep 30, 2014

[Bioc-devel] new package build problems

1 msg Sep 30

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Dan Tenenbaum new package build problems Sep 30, 2014

[Bioc-devel] new package build problems

3 msgs Sep 30

K

Karl Stamm new package build problems Sep 29, 2014

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Sander Bollen new package build problems Sep 30, 2014

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Karl Stamm new package build problems Sep 30, 2014

[Bioc-devel] Cannot interact with a BigWig file on the web with rtracklayer (Windows specific)

4 msgs Sep 30

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Leonardo Collado Torres Cannot interact with a BigWig file on the web with rtracklayer (Windows specific) Sep 30, 2014

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Dan Tenenbaum Cannot interact with a BigWig file on the web with rtracklayer (Windows specific) Sep 30, 2014

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Leonardo Collado Torres Cannot interact with a BigWig file on the web with rtracklayer (Windows specific) Sep 30, 2014

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Michael Lawrence Cannot interact with a BigWig file on the web with rtracklayer (Windows specific) Sep 30, 2014

[Bioc-devel] writeVcf performance

15 msgs Sep 30

M

Martin Morgan writeVcf performance Sep 2, 2014

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Michael Lawrence writeVcf performance Sep 2, 2014

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Gabriel Becker writeVcf performance Sep 4, 2014

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Valerie Obenchain writeVcf performance Sep 4, 2014

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Kasper Daniel Hansen writeVcf performance Sep 5, 2014

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Valerie Obenchain writeVcf performance Sep 8, 2014

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Gabriel Becker writeVcf performance Sep 8, 2014

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Valerie Obenchain writeVcf performance Sep 8, 2014

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Valerie Obenchain writeVcf performance Sep 9, 2014

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Hervé Pagès writeVcf performance Sep 9, 2014

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Valerie Obenchain writeVcf performance Sep 9, 2014

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Hervé Pagès writeVcf performance Sep 9, 2014

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Valerie Obenchain writeVcf performance Sep 17, 2014

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Gabriel Becker writeVcf performance Sep 30, 2014

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Valerie Obenchain writeVcf performance Sep 30, 2014

[Bioc-devel] Guidelines for shiny packages

2 msgs Sep 30

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Thomas Lin Pedersen Guidelines for shiny packages Sep 29, 2014

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Shawn Balcome Guidelines for shiny packages Sep 30, 2014

[Bioc-devel] GenomicFiles: chunking

7 msgs Sep 30

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Kasper Daniel Hansen GenomicFiles: chunking Sep 28, 2014

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Kasper Daniel Hansen GenomicFiles: chunking Sep 28, 2014

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Michael Love GenomicFiles: chunking Sep 29, 2014

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Kasper Daniel Hansen GenomicFiles: chunking Sep 29, 2014

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Michael Love GenomicFiles: chunking Sep 29, 2014

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Valerie Obenchain GenomicFiles: chunking Sep 29, 2014

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Michael Love GenomicFiles: chunking Sep 30, 2014

[Bioc-devel] Fwd: hedgehog Subversion server upgrade Tuesday 9/30

5 msgs Sep 30

D

Dan Tenenbaum hedgehog Subversion server upgrade Tuesday 9/30 Sep 29, 2014

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Dan Tenenbaum hedgehog Subversion server upgrade Tuesday 9/30 Sep 30, 2014

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James W. MacDonald hedgehog Subversion server upgrade Tuesday 9/30 Sep 30, 2014

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Dan Tenenbaum hedgehog Subversion server upgrade Tuesday 9/30 Sep 30, 2014

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James W. MacDonald hedgehog Subversion server upgrade Tuesday 9/30 Sep 30, 2014

[Bioc-devel] Problems creating Git-SVN bridge to an organisation repo

1 msg Sep 30

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Dan Tenenbaum Problems creating Git-SVN bridge to an organisation repo Sep 30, 2014

[Bioc-devel] BSgenome forge file input file restrictions

2 msgs Sep 30

H

Hervé Pagès BSgenome forge file input file restrictions Sep 29, 2014

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Hahne, Florian BSgenome forge file input file restrictions Sep 30, 2014

[Bioc-devel] Problems creating Git-SVN bridge to an organisation repo

1 msg Sep 30

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Antti Honkela Problems creating Git-SVN bridge to an organisation repo Sep 30, 2014

[Bioc-devel] new package build problems

1 msg Sep 29

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Dan Tenenbaum new package build problems Sep 29, 2014

[Bioc-devel] GenomicFiles: some random issues

8 msgs Sep 29

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Martin Morgan GenomicFiles: some random issues Sep 29, 2014

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Tim Triche, Jr. GenomicFiles: some random issues Sep 29, 2014

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Michael Lawrence GenomicFiles: some random issues Sep 29, 2014

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Michael Lawrence GenomicFiles: some random issues Sep 29, 2014

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Kasper Daniel Hansen GenomicFiles: some random issues Sep 29, 2014

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Charles C. Berry GenomicFiles: some random issues Sep 29, 2014

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Kasper Daniel Hansen GenomicFiles: some random issues Sep 29, 2014

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Michael Lawrence GenomicFiles: some random issues Sep 29, 2014

[Bioc-devel] BiocParallel-devel error

4 msgs Sep 29

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Thomas Girke BiocParallel-devel error Sep 23, 2014

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Michel Lang BiocParallel-devel error Sep 24, 2014

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Michel Lang BiocParallel-devel error Sep 26, 2014

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Valerie Obenchain BiocParallel-devel error Sep 29, 2014

[Bioc-devel] Guidelines for shiny packages

1 msg Sep 29

D

Dan Tenenbaum Guidelines for shiny packages Sep 29, 2014

[Bioc-devel] Guidelines for shiny packages

1 msg Sep 29

T

Thomas Lin Pedersen Guidelines for shiny packages Sep 29, 2014

[Bioc-devel] Workflows

3 msgs Sep 29

D

Dan Tenenbaum Workflows Sep 29, 2014

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Wolfgang Huber Workflows Sep 29, 2014

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Dan Tenenbaum Workflows Sep 29, 2014

[Bioc-devel] Workflows

1 msg Sep 29

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Wolfgang Huber Workflows Sep 29, 2014

[Bioc-devel] BSgenome forge file input file restrictions

1 msg Sep 29

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Hahne, Florian BSgenome forge file input file restrictions Sep 29, 2014

[Bioc-devel] GenomicFiles: some random issues

2 msgs Sep 28

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Kasper Daniel Hansen GenomicFiles: some random issues Sep 28, 2014

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Kasper Daniel Hansen GenomicFiles: some random issues Sep 28, 2014

[Bioc-devel] minor suggestion for BiocStyle?

7 msgs Sep 28

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Ramon Diaz-Uriarte minor suggestion for BiocStyle? Sep 26, 2014

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Andrzej Oleś minor suggestion for BiocStyle? Sep 27, 2014

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Ramon Diaz-Uriarte minor suggestion for BiocStyle? Sep 27, 2014

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Martin Morgan minor suggestion for BiocStyle? Sep 27, 2014

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Wolfgang Huber minor suggestion for BiocStyle? Sep 28, 2014

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Andrzej Oleś minor suggestion for BiocStyle? Sep 28, 2014

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Kasper Daniel Hansen minor suggestion for BiocStyle? Sep 28, 2014

[Bioc-devel] support site

6 msgs Sep 26

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Kasper Daniel Hansen support site Sep 26, 2014

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Wolfgang Huber support site Sep 26, 2014

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Martin Morgan support site Sep 26, 2014

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Michael Lawrence support site Sep 26, 2014

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Steve Lianoglou support site Sep 26, 2014

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Henrik Bengtsson support site Sep 26, 2014

[Bioc-devel] Important news about pending updates to the RSQLite package

1 msg Sep 26

D

Dan Tenenbaum Important news about pending updates to the RSQLite package Sep 26, 2014

[Bioc-devel] upcoming deadlines

1 msg Sep 25

D

Dan Tenenbaum upcoming deadlines Sep 25, 2014

[Bioc-devel] Helping with moderation/cleanup of the support site

4 msgs Sep 24

S

Steve Lianoglou Helping with moderation/cleanup of the support site Sep 24, 2014

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Sean Davis Helping with moderation/cleanup of the support site Sep 24, 2014

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Dan Tenenbaum Helping with moderation/cleanup of the support site Sep 24, 2014

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Dan Tenenbaum Helping with moderation/cleanup of the support site Sep 24, 2014

[Bioc-devel] deprecated org.Hs.egCHRLOC

5 msgs Sep 23

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rcaloger deprecated org.Hs.egCHRLOC Sep 23, 2014

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Vincent Carey deprecated org.Hs.egCHRLOC Sep 23, 2014

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rcaloger deprecated org.Hs.egCHRLOC Sep 23, 2014

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rcaloger deprecated org.Hs.egCHRLOC UPDATE: the as.list() behaves differently in stable and devel configuration Sep 23, 2014

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Marc Carlson deprecated org.Hs.egCHRLOC UPDATE: the as.list() behaves differently in stable and devel configuration Sep 23, 2014

[Bioc-devel] BiocParallel-devel error

2 msgs Sep 23

V

Valerie Obenchain BiocParallel-devel error Sep 22, 2014

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Valerie Obenchain BiocParallel-devel error Sep 23, 2014

[Bioc-devel] Importing summary from AnnotationDbi, Category, GOstats

5 msgs Sep 23

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Hervé Pagès Importing summary from AnnotationDbi, Category, GOstats Sep 23, 2014

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James W. MacDonald Importing summary from AnnotationDbi, Category, GOstats Sep 23, 2014

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James W. MacDonald Importing summary from AnnotationDbi, Category, GOstats Sep 23, 2014

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Hervé Pagès Importing summary from AnnotationDbi, Category, GOstats Sep 23, 2014

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James W. MacDonald Importing summary from AnnotationDbi, Category, GOstats Sep 23, 2014

[Bioc-devel] new error(?) related to annotation: illuminaHumanv1CHR is deprecated

6 msgs Sep 23

V

Vincent Carey new error(?) related to annotation: illuminaHumanv1CHR is deprecated Sep 21, 2014

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Martin Morgan new error(?) related to annotation: illuminaHumanv1CHR is deprecated Sep 21, 2014

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Vincent Carey new error(?) related to annotation: illuminaHumanv1CHR is deprecated Sep 21, 2014

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Marc Carlson new error(?) related to annotation: illuminaHumanv1CHR is deprecated Sep 22, 2014

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Vincent Carey new error(?) related to annotation: illuminaHumanv1CHR is deprecated Sep 22, 2014

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Marc Carlson new error(?) related to annotation: illuminaHumanv1CHR is deprecated Sep 23, 2014

[Bioc-devel] Git-SVN bridge: Alternative to get commit history?

4 msgs Sep 23

D

Dan Tenenbaum Git-SVN bridge: Alternative to get commit history? Sep 21, 2014

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Henrik Bengtsson Git-SVN bridge: Alternative to get commit history? Sep 22, 2014

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Sean Davis Git-SVN bridge: Alternative to get commit history? Sep 23, 2014

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Henrik Bengtsson Git-SVN bridge: Alternative to get commit history? Sep 23, 2014

[Bioc-devel] Importing summary from AnnotationDbi, Category, GOstats

1 msg Sep 23

J

James W. MacDonald Importing summary from AnnotationDbi, Category, GOstats Sep 23, 2014

[Bioc-devel] Changing the name of a package

5 msgs Sep 23

D

Dan Tenenbaum Changing the name of a package Sep 10, 2014

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Tom Hardcastle Changing the name of a package Sep 11, 2014

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Dan Tenenbaum Changing the name of a package Sep 11, 2014

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Tom Hardcastle Changing the name of a package Sep 23, 2014

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Dan Tenenbaum Changing the name of a package Sep 23, 2014

[Bioc-devel] Documentation Link to S4 Class from Package in Suggests Field

2 msgs Sep 22

D

Dario Strbenac Documentation Link to S4 Class from Package in Suggests Field Sep 22, 2014

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Michael Lawrence Documentation Link to S4 Class from Package in Suggests Field Sep 22, 2014

[Bioc-devel] 'semantically rich' subsetting of SummarizedExperiments

11 msgs Sep 22

V

Vincent Carey 'semantically rich' subsetting of SummarizedExperiments Sep 20, 2014

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Sean Davis 'semantically rich' subsetting of SummarizedExperiments Sep 20, 2014

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Tim Triche, Jr. 'semantically rich' subsetting of SummarizedExperiments Sep 20, 2014

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Vincent Carey 'semantically rich' subsetting of SummarizedExperiments Sep 20, 2014

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Gabriel Becker 'semantically rich' subsetting of SummarizedExperiments Sep 20, 2014

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Sean Davis 'semantically rich' subsetting of SummarizedExperiments Sep 20, 2014

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Vincent Carey 'semantically rich' subsetting of SummarizedExperiments Sep 20, 2014

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Gabriel Becker 'semantically rich' subsetting of SummarizedExperiments Sep 20, 2014

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Vincent Carey 'semantically rich' subsetting of SummarizedExperiments Sep 21, 2014

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Cook, Malcolm 'semantically rich' subsetting of SummarizedExperiments Sep 22, 2014

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Vincent Carey 'semantically rich' subsetting of SummarizedExperiments Sep 22, 2014

[Bioc-devel] coerce ExpressionSet to SummarizedExperiment

6 msgs Sep 21

V

Vincent Carey coerce ExpressionSet to SummarizedExperiment Sep 20, 2014

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Sean Davis coerce ExpressionSet to SummarizedExperiment Sep 20, 2014

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Martin Morgan coerce ExpressionSet to SummarizedExperiment Sep 20, 2014

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Michael Love coerce ExpressionSet to SummarizedExperiment Sep 20, 2014

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Hector Corrada Bravo coerce ExpressionSet to SummarizedExperiment Sep 20, 2014

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Hervé Pagès coerce ExpressionSet to SummarizedExperiment Sep 21, 2014

[Bioc-devel] Git-SVN bridge: Alternative to get commit history?

1 msg Sep 21

H

Henrik Bengtsson Git-SVN bridge: Alternative to get commit history? Sep 21, 2014

[Bioc-devel] Warning "Register native routines" during BiocCheck

2 msgs Sep 21

G

Gabriel Becker Warning "Register native routines" during BiocCheck Sep 21, 2014

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Kevin Ushey Warning "Register native routines" during BiocCheck Sep 21, 2014

[Bioc-devel] Warning "Register native routines" during BiocCheck

3 msgs Sep 21

张

张雨晴 Warning "Register native routines" during BiocCheck Sep 21, 2014

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Martin Morgan Warning "Register native routines" during BiocCheck Sep 21, 2014

张

张雨晴 Warning "Register native routines" during BiocCheck Sep 21, 2014

[Bioc-devel] anyone needs access to an OS X Mavericks machine?

1 msg Sep 21

K

Kasper Daniel Hansen anyone needs access to an OS X Mavericks machine? Sep 21, 2014

[Bioc-devel] BiocParallel-devel error

1 msg Sep 20

T

Thomas Girke BiocParallel-devel error Sep 20, 2014

[Bioc-devel] hedgehog Subversion server upgrade Tuesday 9/30

3 msgs Sep 20

D

Dan Tenenbaum hedgehog Subversion server upgrade Tuesday 9/30 Sep 17, 2014

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Kasper Daniel Hansen hedgehog Subversion server upgrade Tuesday 9/30 Sep 17, 2014

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Dan Tenenbaum hedgehog Subversion server upgrade Tuesday 9/30 Sep 20, 2014

[Bioc-devel] thanks

1 msg Sep 19

V

Valerie Obenchain thanks Sep 19, 2014

[Bioc-devel] need for consistent coordinate mapping API

3 msgs Sep 19

M

Michael Lawrence need for consistent coordinate mapping API Sep 19, 2014

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Laurent Gatto need for consistent coordinate mapping API Sep 19, 2014

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Hervé Pagès need for consistent coordinate mapping API Sep 19, 2014

[Bioc-devel] GenomicRanges::findOverlaps() ignoring chromosome information?

3 msgs Sep 19

K

Kevin Rue-Albrecht GenomicRanges::findOverlaps() ignoring chromosome information? Sep 19, 2014

K

Kevin Rue-Albrecht GenomicRanges::findOverlaps() ignoring chromosome information? Sep 19, 2014

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Kevin Rue-Albrecht GenomicRanges::findOverlaps() ignoring chromosome information? Sep 19, 2014

[Bioc-devel] mis-spelled BiocViews term

2 msgs Sep 18

L

Levi Waldron mis-spelled BiocViews term Sep 18, 2014

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Arora, Sonali mis-spelled BiocViews term Sep 18, 2014

[Bioc-devel] The release is fast approaching. Information about upcoming deadlines.

1 msg Sep 17

M

Marc Carlson The release is fast approaching. Information about upcoming deadlines. Sep 17, 2014

[Bioc-devel] read fcs file from CyTOF with

1 msg Sep 16

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Josef Spidlen read fcs file from CyTOF with Sep 16, 2014

[Bioc-devel] BiocCheck crash with package vignette?

2 msgs Sep 15

D

Dan Tenenbaum BiocCheck crash with package vignette? Sep 15, 2014

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Leo Lahti BiocCheck crash with package vignette? Sep 15, 2014

[Bioc-devel] BiocCheck crash with package vignette?

1 msg Sep 15

L

Leo Lahti BiocCheck crash with package vignette? Sep 15, 2014

[Bioc-devel] [BioC] Course: Learning R / Bioconductor for Sequence Analysis, Seattle, WA Oct 27-29

1 msg Sep 15

M

Martin Morgan Course: Learning R / Bioconductor for Sequence Analysis, Seattle, WA Oct 27-29 Sep 15, 2014

[Bioc-devel] Course: Learning R / Bioconductor for Sequence Analysis, Seattle, WA Oct 27-29

1 msg Sep 15

M

Martin Morgan Course: Learning R / Bioconductor for Sequence Analysis, Seattle, WA Oct 27-29 Sep 15, 2014

[Bioc-devel] important announcement

1 msg Sep 12

M

Marc Carlson important announcement Sep 12, 2014

[Bioc-devel] Fwd: read fcs file from CyTOF with

1 msg Sep 12

M

Mike read fcs file from CyTOF with Sep 12, 2014

[Bioc-devel] AnnotatioDbi Biostrings load order breaks GenomicFiles summary method

1 msg Sep 12

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Dan Tenenbaum AnnotatioDbi Biostrings load order breaks GenomicFiles summary method Sep 12, 2014

[Bioc-devel] AnnotatioDbi Biostrings load order breaks GenomicFiles summary method

1 msg Sep 12

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Marcin Cieślik AnnotatioDbi Biostrings load order breaks GenomicFiles summary method Sep 12, 2014

[Bioc-devel] read fcs file from CyTOF with

1 msg Sep 12

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Hurlimann Niklaus read fcs file from CyTOF with Sep 12, 2014

[Bioc-devel] some turbulences due to IRanges/S4Vectors split

1 msg Sep 11

H

Hervé Pagès some turbulences due to IRanges/S4Vectors split Sep 11, 2014

[Bioc-devel] biocLite message "R package not available" is confusing

4 msgs Sep 10

M

Martin Morgan biocLite message "R package not available" is confusing Sep 10, 2014

D

Davide Risso biocLite message "R package not available" is confusing Sep 10, 2014

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Martin Morgan biocLite message "R package not available" is confusing Sep 10, 2014

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Davide Risso biocLite message "R package not available" is confusing Sep 10, 2014

[Bioc-devel] Please bump version number when committing changes

13 msgs Sep 10

D

Dan Tenenbaum Please bump version number when committing changes Sep 4, 2014

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Stephanie M. Gogarten Please bump version number when committing changes Sep 5, 2014

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Dan Tenenbaum Please bump version number when committing changes Sep 5, 2014

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Gabriel Becker Please bump version number when committing changes Sep 5, 2014

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Peter Haverty Please bump version number when committing changes Sep 5, 2014

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Ryan Please bump version number when committing changes Sep 5, 2014

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Peter Haverty Please bump version number when committing changes Sep 5, 2014

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Vincent Carey Please bump version number when committing changes Sep 5, 2014

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Michael Lawrence Please bump version number when committing changes Sep 5, 2014

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Kasper Daniel Hansen Please bump version number when committing changes Sep 5, 2014

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Dan Tenenbaum Please bump version number when committing changes Sep 5, 2014

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Gabriel Becker Please bump version number when committing changes Sep 8, 2014

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Martin Morgan Please bump version number when committing changes Sep 10, 2014

[Bioc-devel] biocLite message "R package not available" is confusing

1 msg Sep 10

D

Davide Risso biocLite message "R package not available" is confusing Sep 10, 2014

[Bioc-devel] Fwd: [JOB] NIH-Wide Stadtman Tenure-Track Recruitment

1 msg Sep 10

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Sean Davis NIH-Wide Stadtman Tenure-Track Recruitment Sep 10, 2014

[Bioc-devel] [JOB] NIH-Wide Stadtman Tenure-Track Recruitment

1 msg Sep 10

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Sean Davis NIH-Wide Stadtman Tenure-Track Recruitment Sep 10, 2014

[Bioc-devel] should genome() be so complicated?/add genome report to GRanges show method

10 msgs Sep 9

P

Peter Hickey should genome() be so complicated?/add genome report to GRanges show method Sep 8, 2014

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Hervé Pagès should genome() be so complicated?/add genome report to GRanges show method Sep 8, 2014

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Peter Hickey should genome() be so complicated?/add genome report to GRanges show method Sep 8, 2014

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Michael Lawrence should genome() be so complicated?/add genome report to GRanges show method Sep 8, 2014

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Hervé Pagès should genome() be so complicated?/add genome report to GRanges show method Sep 8, 2014

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Vincent Carey should genome() be so complicated?/add genome report to GRanges show method Sep 8, 2014

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Michael Lawrence should genome() be so complicated?/add genome report to GRanges show method Sep 9, 2014

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Martin Morgan should genome() be so complicated?/add genome report to GRanges show method Sep 9, 2014

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Michael Lawrence should genome() be so complicated?/add genome report to GRanges show method Sep 9, 2014

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Hervé Pagès should genome() be so complicated?/add genome report to GRanges show method Sep 9, 2014

[Bioc-devel] daily build system behind

2 msgs Sep 9

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Levi Waldron daily build system behind Sep 9, 2014

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Andrzej Oleś daily build system behind Sep 9, 2014

[Bioc-devel] Changing the name of a package

1 msg Sep 8

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Thomas J Hardcastle Changing the name of a package Sep 8, 2014

[Bioc-devel] should genome() be so complicated?/add genome report to GRanges show method

4 msgs Sep 8

H

Hervé Pagès should genome() be so complicated?/add genome report to GRanges show method Sep 8, 2014

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Vincent Carey should genome() be so complicated?/add genome report to GRanges show method Sep 8, 2014

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Michael Lawrence should genome() be so complicated?/add genome report to GRanges show method Sep 8, 2014

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Hervé Pagès should genome() be so complicated?/add genome report to GRanges show method Sep 8, 2014

[Bioc-devel] should genome() be so complicated?/add genome report to GRanges show method

1 msg Sep 8

V

Vincent Carey should genome() be so complicated?/add genome report to GRanges show method Sep 8, 2014

[Bioc-devel] bug when coercing from list to SimpleList

2 msgs Sep 5

H

Hervé Pagès bug when coercing from list to SimpleList Sep 5, 2014

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Michael Lawrence bug when coercing from list to SimpleList Sep 5, 2014

[Bioc-devel] Bioconductor 3.0 release schedule now available

1 msg Sep 4

D

Dan Tenenbaum Bioconductor 3.0 release schedule now available Sep 4, 2014

[Bioc-devel] Announcement about the new support site

1 msg Sep 4

M

Marc Carlson Announcement about the new support site Sep 4, 2014

[Bioc-devel] Submitting a workflow

5 msgs Sep 3

M

Michael Love Submitting a workflow Sep 3, 2014

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Vincent Carey Submitting a workflow Sep 3, 2014

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Andrzej Oleś Submitting a workflow Sep 3, 2014

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Michael Love Submitting a workflow Sep 3, 2014

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Dan Tenenbaum Submitting a workflow Sep 3, 2014

[Bioc-devel] Valid classes for extraColumnSlots

2 msgs Sep 2

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Peter Hickey Valid classes for extraColumnSlots Sep 2, 2014

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Dan Tenenbaum Valid classes for extraColumnSlots Sep 2, 2014