Bioc-devel - April 2015 - Subject View

'memory not mapped' in trimLRpatterns

2 msgs · Apr 30 – Apr 30

Michael Stadler 'memory not mapped' in trimLRpatterns Apr 30, 2015 Hervé Pagès 'memory not mapped' in trimLRpatterns Apr 30, 2015

AnnotationHub: Error in Docker release_core

3 msgs · Apr 9 – Apr 9

Ludwig Geistlinger AnnotationHub: Error in Docker release_core Apr 9, 2015 Elena Grassi AnnotationHub: Error in Docker release_core Apr 9, 2015 Ludwig Geistlinger AnnotationHub: Error in Docker release_core Apr 9, 2015

AnnotationHub: ExpressionSetResource Error in Docker devel_core

5 msgs · Apr 9 – Apr 10

Ludwig Geistlinger AnnotationHub: ExpressionSetResource Error in Docker devel_core Apr 9, 2015 Vincent Carey AnnotationHub: ExpressionSetResource Error in Docker devel_core Apr 9, 2015 Ludwig Geistlinger AnnotationHub: ExpressionSetResource Error in Docker devel_core Apr 9, 2015 Martin Morgan AnnotationHub: ExpressionSetResource Error in Docker devel_core Apr 9, 2015 Ludwig Geistlinger AnnotationHub: ExpressionSetResource Error in Docker devel_core Apr 10, 2015

AnnotationHubData Error: Access denied: 530

20 msgs · Apr 9 – Apr 17

Announcing a new package: DMRcaller

1 msg · Apr 8

Radu Zabet Announcing a new package: DMRcaller Apr 8, 2015

Announcing a new package: FlowRepositoryR

1 msg · Apr 9

Josef Spidlen Announcing a new package: FlowRepositoryR Apr 9, 2015

Announcing a new package: GoogleGenomics

1 msg · Apr 24

Siddhartha Bagaria Announcing a new package: GoogleGenomics Apr 24, 2015

Announcing a new package: R3CPET

1 msg · Apr 9

Djekidel Mohamed Nadhir Announcing a new package: R3CPET Apr 9, 2015

Announcing a new package: ggtree

1 msg · Apr 9

Yu, Guangchuang Announcing a new package: ggtree Apr 9, 2015

Announcing a new package: regioneR

1 msg · Apr 2

Bernat Gel Announcing a new package: regioneR Apr 2, 2015

Append/combine option for filterFastq and similar?

7 msgs · Apr 21 – Apr 22

Ryan Append/combine option for filterFastq and similar? Apr 21, 2015 Martin Morgan Append/combine option for filterFastq and similar? Apr 21, 2015 Aedin Culhane Append/combine option for filterFastq and similar? Apr 22, 2015 Ryan Append/combine option for filterFastq and similar? Apr 22, 2015 Jim Hester Append/combine option for filterFastq and similar? Apr 22, 2015 Ryan Append/combine option for filterFastq and similar? Apr 22, 2015 Martin Morgan Append/combine option for filterFastq and similar? Apr 22, 2015

BioC 2015 Bioconductor Annual Conference

1 msg · Apr 23

Martin Morgan BioC 2015 Bioconductor Annual Conference Apr 23, 2015

BioC 2015 Conference Posters

1 msg · Apr 24

Valerie Obenchain BioC 2015 Conference Posters Apr 24, 2015

BioC 3.1 branch created

8 msgs · Apr 16 – Apr 17

Dan Tenenbaum BioC 3.1 branch created Apr 16, 2015 Henrik Bengtsson BioC 3.1 branch created Apr 16, 2015 Dan Tenenbaum BioC 3.1 branch created Apr 16, 2015 Henrik Bengtsson BioC 3.1 branch created Apr 16, 2015 Martin, Tiphaine BioC 3.1 branch created Apr 17, 2015 Kevin Rue-Albrecht BioC 3.1 branch created Apr 17, 2015 Martin, Tiphaine BioC 3.1 branch created Apr 17, 2015 Dan Tenenbaum BioC 3.1 branch created Apr 17, 2015

Biobase: Imports repeats Depends

3 msgs · Apr 25 – Apr 27

Henrik Bengtsson Biobase: Imports repeats Depends Apr 25, 2015 Hervé Pagès Biobase: Imports repeats Depends Apr 27, 2015 Henrik Bengtsson Biobase: Imports repeats Depends Apr 27, 2015

Bioc package pages: List also BugReports for a package?

3 msgs · Apr 26 – Apr 27

Henrik Bengtsson Bioc package pages: List also BugReports for a package? Apr 26, 2015 Dan Tenenbaum Bioc package pages: List also BugReports for a package? Apr 27, 2015 Henrik Bengtsson Bioc package pages: List also BugReports for a package? Apr 27, 2015

Bioconductor 3.1 is released!

1 msg · Apr 17

Dan Tenenbaum Bioconductor 3.1 is released! Apr 17, 2015

Bioconductor Newsletter - April 2015

1 msg · Apr 3

Valerie Obenchain Bioconductor Newsletter - April 2015 Apr 3, 2015

Biostring

2 msgs · Apr 26 – Apr 26

a_kinga at yahoo.com Biostring Apr 26, 2015 Martin Morgan Biostring Apr 26, 2015

BrowserViz

4 msgs · Apr 3 – Apr 3

Michael Lawrence BrowserViz Apr 3, 2015 Michael Lawrence BrowserViz Apr 3, 2015 Michael Lawrence BrowserViz Apr 3, 2015 Hector Corrada Bravo BrowserViz Apr 3, 2015

BrowserViz and sub-protocols

7 msgs · Apr 6 – Apr 6

Michael Lawrence BrowserViz and sub-protocols Apr 6, 2015 Tim Triche, Jr. BrowserViz and sub-protocols Apr 6, 2015 Michael Lawrence BrowserViz and sub-protocols Apr 6, 2015 Dan Tenenbaum BrowserViz and sub-protocols Apr 6, 2015 Michael Lawrence BrowserViz and sub-protocols Apr 6, 2015 Tim Triche, Jr. BrowserViz and sub-protocols Apr 6, 2015 Tim Triche, Jr. BrowserViz and sub-protocols Apr 6, 2015

BrowserViz: curious but needs a small tweak to run example

1 msg · Apr 3

Leonardo Collado Torres BrowserViz: curious but needs a small tweak to run example Apr 3, 2015

Build error for DESeq2 dev causing error in other package builds

3 msgs · Apr 3 – Apr 3

Andrea Rau Build error for DESeq2 dev causing error in other package builds Apr 3, 2015 Michael Love Build error for DESeq2 dev causing error in other package builds Apr 3, 2015 Martin Morgan Build error for DESeq2 dev causing error in other package builds Apr 3, 2015

Changes to the SummarizedExperiment Class

4 msgs · Apr 1 – Apr 1

Michael Love Changes to the SummarizedExperiment Class Apr 1, 2015 Hervé Pagès Changes to the SummarizedExperiment Class Apr 1, 2015 Michael Love Changes to the SummarizedExperiment Class Apr 1, 2015 Martin Morgan Changes to the SummarizedExperiment Class Apr 1, 2015

Dependency issue

4 msgs · Apr 17 – Apr 18

t.kuilman at nki.nl Dependency issue Apr 17, 2015 Dan Tenenbaum Dependency issue Apr 17, 2015 Henrik Bengtsson Dependency issue Apr 18, 2015 Henrik Bengtsson Dependency issue Apr 18, 2015

Disabling commits to release today; Update NEWS files, biocViews

1 msg · Apr 9

Dan Tenenbaum Disabling commits to release today; Update NEWS files, biocViews Apr 9, 2015

Docker granularity: containers for individual R packages, running on a normal R installation?

7 msgs · Apr 14 – Apr 15

Wolfgang Huber Docker granularity: containers for individual R packages, running on a normal R installation? Apr 14, 2015 Sean Davis Docker granularity: containers for individual R packages, running on a normal R installation? Apr 14, 2015 Wolfgang Huber Docker granularity: containers for individual R packages, running on a normal R installation? Apr 14, 2015 Michael Lawrence Docker granularity: containers for individual R packages, running on a normal R installation? Apr 14, 2015 Martin Morgan Docker granularity: containers for individual R packages, running on a normal R installation? Apr 14, 2015 Bastian Schiffthaler Docker granularity: containers for individual R packages, running on a normal R installation? Apr 15, 2015 Dan Tenenbaum Docker granularity: containers for individual R packages, running on a normal R installation? Apr 15, 2015

Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3

6 msgs · Apr 17 – Apr 17

Sergei Ryazansky Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Apr 17, 2015 Peter Haverty Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Apr 17, 2015 Dan Tenenbaum Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Apr 17, 2015 Sergei Ryazansky Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Apr 17, 2015 Dan Tenenbaum Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Apr 17, 2015 Sergei Ryazansky Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Apr 17, 2015

Error on Windows when selecting a single chromosome from a BSgenome

1 msg · Apr 21

Hervé Pagès Error on Windows when selecting a single chromosome from a BSgenome Apr 21, 2015

Important: Bioconductor 3.1 branch to be created today - do not commit during this time

1 msg · Apr 16

Dan Tenenbaum Important: Bioconductor 3.1 branch to be created today - do not commit during this time Apr 16, 2015

Interoperability between DataFrame and dplyr?

8 msgs · Apr 23 – Apr 24

Just for fun

1 msg · Apr 26

Sean Davis Just for fun Apr 26, 2015

MafDb.ExAC.r0.3.sites missing from build

3 msgs · Apr 10 – Apr 10

Robert Castelo MafDb.ExAC.r0.3.sites missing from build Apr 10, 2015 Dan Tenenbaum MafDb.ExAC.r0.3.sites missing from build Apr 10, 2015 Robert Castelo MafDb.ExAC.r0.3.sites missing from build Apr 10, 2015

New package for copy number detection from targeted sequencing using off-target reads

1 msg · Apr 9

t.kuilman at nki.nl New package for copy number detection from targeted sequencing using off-target reads Apr 9, 2015

New package: coMET

2 msgs · Apr 8 – Apr 10

Hervé Pagès New package: coMET Apr 8, 2015 Martin, Tiphaine New package: coMET Apr 10, 2015

New-package: bamsignals

1 msg · Apr 23

Alessandro Mammana New-package: bamsignals Apr 23, 2015

OpenMP on Mac OS "Mavericks" build server morelia

4 msgs · Apr 13 – Apr 13

Ulrich Bodenhofer OpenMP on Mac OS "Mavericks" build server morelia Apr 13, 2015 Dan Tenenbaum OpenMP on Mac OS "Mavericks" build server morelia Apr 13, 2015 Ulrich Bodenhofer OpenMP on Mac OS "Mavericks" build server morelia Apr 13, 2015 Dan Tenenbaum OpenMP on Mac OS "Mavericks" build server morelia Apr 13, 2015

Proposed biocViews for Hi-C assay

2 msgs · Apr 9 – Apr 14

Nathaniel Hayden Proposed biocViews for Hi-C assay Apr 9, 2015 Nathaniel Hayden Proposed biocViews for Hi-C assay Apr 14, 2015

R 3.3 for snow leopard

6 msgs · Apr 17 – Apr 20

Leonardo Collado Torres R 3.3 for snow leopard Apr 17, 2015 Dan Tenenbaum R 3.3 for snow leopard Apr 17, 2015 Nicolas Delhomme R 3.3 for snow leopard Apr 17, 2015 Dan Tenenbaum R 3.3 for snow leopard Apr 20, 2015 Dan Tenenbaum R 3.3 for snow leopard Apr 20, 2015 Leonardo Collado Torres R 3.3 for snow leopard Apr 20, 2015

Short URLs for packages?

5 msgs · Apr 28 – Apr 30

Dan Tenenbaum Short URLs for packages? Apr 28, 2015 Steve Lianoglou Short URLs for packages? Apr 28, 2015 Dan Tenenbaum Short URLs for packages? Apr 28, 2015 Robert Castelo Short URLs for packages? Apr 30, 2015 Dan Tenenbaum Short URLs for packages? Apr 30, 2015

Suggestion: export function fetchChromLengthsFromEnsembl in GenomicFeatures

2 msgs · Apr 11 – Apr 11

Rainer Johannes Suggestion: export function fetchChromLengthsFromEnsembl in GenomicFeatures Apr 11, 2015 Hervé Pagès Suggestion: export function fetchChromLengthsFromEnsembl in GenomicFeatures Apr 11, 2015

SummarizedExperiment subset of 4 dimensions

5 msgs · Apr 1 – Apr 6

Jesper Gådin SummarizedExperiment subset of 4 dimensions Apr 1, 2015 Michael Lawrence SummarizedExperiment subset of 4 dimensions Apr 1, 2015 Martin Morgan SummarizedExperiment subset of 4 dimensions Apr 1, 2015 Martin Morgan SummarizedExperiment subset of 4 dimensions Apr 1, 2015 Jesper Gådin SummarizedExperiment subset of 4 dimensions Apr 6, 2015

SummarizedExperiment, differing assay dimnames

2 msgs · Apr 3 – Apr 3

Michael Love SummarizedExperiment, differing assay dimnames Apr 3, 2015 Michael Love SummarizedExperiment, differing assay dimnames Apr 3, 2015

Update GSEABase to support new MSigDB collection in v5.0

2 msgs · Apr 16 – Apr 16

Steve Lianoglou Update GSEABase to support new MSigDB collection in v5.0 Apr 16, 2015 Martin Morgan Update GSEABase to support new MSigDB collection in v5.0 Apr 16, 2015

Updating package NEWS files for Bioconductor 3.1 release announcement (and biocViews)

1 msg · Apr 1

Dan Tenenbaum Updating package NEWS files for Bioconductor 3.1 release announcement (and biocViews) Apr 1, 2015

Use of confounders in downstream analysis

4 msgs · Apr 21 – Apr 21

Aileen Bahl Use of confounders in downstream analysis Apr 21, 2015 Sean Davis Use of confounders in downstream analysis Apr 21, 2015 Aileen Bahl Use of confounders in downstream analysis Apr 21, 2015 Kasper Daniel Hansen Use of confounders in downstream analysis Apr 21, 2015

Warning message: multiple methods tables found for ‘score’

9 msgs · Apr 10 – Apr 10

Warnings from ls() in AnnotationDbi

2 msgs · Apr 24 – Apr 24

James W. MacDonald Warnings from ls() in AnnotationDbi Apr 24, 2015 Martin Morgan Warnings from ls() in AnnotationDbi Apr 24, 2015

as.character method for GenomicRanges?

14 msgs · Apr 24 – Apr 27

biocUpgrade Wrongly Infers R Version

2 msgs · Apr 27 – Apr 27

Dario Strbenac biocUpgrade Wrongly Infers R Version Apr 27, 2015 Dan Tenenbaum biocUpgrade Wrongly Infers R Version Apr 27, 2015

build error, piano package

3 msgs · Apr 21 – Apr 22

Leif Väremo build error, piano package Apr 21, 2015 Dan Tenenbaum build error, piano package Apr 22, 2015 Kasper Daniel Hansen build error, piano package Apr 22, 2015

building R and bioconductor

5 msgs · Apr 28 – Apr 28

Berri, Stefano building R and bioconductor Apr 28, 2015 Laurent Gatto building R and bioconductor Apr 28, 2015 Martin Morgan building R and bioconductor Apr 28, 2015 Gabriel Becker building R and bioconductor Apr 28, 2015 Gabriel Becker building R and bioconductor Apr 28, 2015

coverage(gr, weight='score') does not work when score(gr) is an Rle

7 msgs · Apr 17 – Apr 20

Philip Lijnzaad coverage(gr, weight='score') does not work when score(gr) is an Rle Apr 17, 2015 Michael Lawrence coverage(gr, weight='score') does not work when score(gr) is an Rle Apr 17, 2015 Hervé Pagès coverage(gr, weight='score') does not work when score(gr) is an Rle Apr 17, 2015 Michael Lawrence coverage(gr, weight='score') does not work when score(gr) is an Rle Apr 17, 2015 Hervé Pagès coverage(gr, weight='score') does not work when score(gr) is an Rle Apr 17, 2015 Michael Lawrence coverage(gr, weight='score') does not work when score(gr) is an Rle Apr 17, 2015 Hervé Pagès coverage(gr, weight='score') does not work when score(gr) is an Rle Apr 20, 2015

issue about S4 slot has a dist object.

8 msgs · Apr 1 – Apr 2

mapping variadic calls to binary calls for dispatch

1 msg · Apr 22

Michael Lawrence mapping variadic calls to binary calls for dispatch Apr 22, 2015

namespace 'GenomeInfoDb' is not available

2 msgs · Apr 29 – Apr 29

Chenglin Liu namespace 'GenomeInfoDb' is not available Apr 29, 2015 Martin Morgan namespace 'GenomeInfoDb' is not available Apr 29, 2015

recalling methods

2 msgs · Apr 6 – Apr 6

Michael Love recalling methods Apr 6, 2015 Leonardo Collado Torres recalling methods Apr 6, 2015

request for more notices about build issues

6 msgs · Apr 8 – Apr 15

Michael Love request for more notices about build issues Apr 8, 2015 Dan Tenenbaum request for more notices about build issues Apr 8, 2015 Sean Davis request for more notices about build issues Apr 8, 2015 Dan Tenenbaum request for more notices about build issues Apr 14, 2015 Michael Love request for more notices about build issues Apr 14, 2015 Kasper Daniel Hansen request for more notices about build issues Apr 15, 2015

scanBam() segfault error

4 msgs · Apr 17 – Apr 20

Leonard Goldstein scanBam() segfault error Apr 17, 2015 Martin Morgan scanBam() segfault error Apr 17, 2015 Martin Morgan scanBam() segfault error Apr 20, 2015 Leonard Goldstein scanBam() segfault error Apr 20, 2015

seqnames as a candidate for BiocGenerics

4 msgs · Apr 26 – Apr 27

Nicolas Delhomme seqnames as a candidate for BiocGenerics Apr 26, 2015 Hervé Pagès seqnames as a candidate for BiocGenerics Apr 27, 2015 Michael Lawrence seqnames as a candidate for BiocGenerics Apr 27, 2015 Nicolas Delhomme seqnames as a candidate for BiocGenerics Apr 27, 2015

today's devel build report

1 msg · Apr 20

Dan Tenenbaum today's devel build report Apr 20, 2015

unsubcribe

1 msg · Apr 27

Le Quan Ly unsubcribe Apr 27, 2015

Bioc-devel April 2015

'memory not mapped' in trimLRpatterns

AnnotationHub: Error in Docker release_core

AnnotationHub: ExpressionSetResource Error in Docker devel_core

AnnotationHubData Error: Access denied: 530

Announcing a new package: DMRcaller

Announcing a new package: FlowRepositoryR

Announcing a new package: GoogleGenomics

Announcing a new package: R3CPET

Announcing a new package: ggtree

Announcing a new package: regioneR

Append/combine option for filterFastq and similar?

BioC 2015 Bioconductor Annual Conference

BioC 2015 Conference Posters

BioC 3.1 branch created

Biobase: Imports repeats Depends

Bioc package pages: List also BugReports for a package?

Bioconductor 3.1 is released!

Bioconductor Newsletter - April 2015

Biostring

BrowserViz

BrowserViz and sub-protocols

BrowserViz: curious but needs a small tweak to run example

Build error for DESeq2 dev causing error in other package builds

Changes to the SummarizedExperiment Class

Dependency issue

Disabling commits to release today; Update NEWS files, biocViews

Docker granularity: containers for individual R packages, running on a normal R installation?

Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3

Error on Windows when selecting a single chromosome from a BSgenome

Important: Bioconductor 3.1 branch to be created today - do not commit during this time

Interoperability between DataFrame and dplyr?

Just for fun

MafDb.ExAC.r0.3.sites missing from build

New package for copy number detection from targeted sequencing using off-target reads

New package: coMET

New-package: bamsignals

OpenMP on Mac OS "Mavericks" build server morelia

Proposed biocViews for Hi-C assay

R 3.3 for snow leopard

Short URLs for packages?

Suggestion: export function fetchChromLengthsFromEnsembl in GenomicFeatures

SummarizedExperiment subset of 4 dimensions

SummarizedExperiment, differing assay dimnames

Update GSEABase to support new MSigDB collection in v5.0

Updating package NEWS files for Bioconductor 3.1 release announcement (and biocViews)

Use of confounders in downstream analysis

Warning message: multiple methods tables found for ‘score’

Warnings from ls() in AnnotationDbi

as.character method for GenomicRanges?

biocUpgrade Wrongly Infers R Version

build error, piano package

building R and bioconductor

coverage(gr, weight='score') does not work when score(gr) is an Rle

issue about S4 slot has a dist object.

mapping variadic calls to binary calls for dispatch

namespace 'GenomeInfoDb' is not available

recalling methods

request for more notices about build issues

scanBam() segfault error

seqnames as a candidate for BiocGenerics

today's devel build report

unsubcribe