Bioc-devel - April 2015 - Date View

Thursday, April 30, 2015 4 emails

Hervé Pagès 'memory not mapped' in trimLRpatterns Michael Stadler 'memory not mapped' in trimLRpatterns Dan Tenenbaum Short URLs for packages? Robert Castelo Short URLs for packages?

Wednesday, April 29, 2015 2 emails

Martin Morgan namespace 'GenomeInfoDb' is not available Chenglin Liu namespace 'GenomeInfoDb' is not available

Tuesday, April 28, 2015 8 emails

Dan Tenenbaum Short URLs for packages? Steve Lianoglou Short URLs for packages? Dan Tenenbaum Short URLs for packages? Gabriel Becker building R and bioconductor Gabriel Becker building R and bioconductor Martin Morgan building R and bioconductor Laurent Gatto building R and bioconductor Berri, Stefano building R and bioconductor

Monday, April 27, 2015 13 emails

Henrik Bengtsson Biobase: Imports repeats Depends Henrik Bengtsson Bioc package pages: List also BugReports for a package? Dan Tenenbaum biocUpgrade Wrongly Infers R Version Dario Strbenac biocUpgrade Wrongly Infers R Version Dan Tenenbaum Bioc package pages: List also BugReports for a package? Hervé Pagès Biobase: Imports repeats Depends Hervé Pagès as.character method for GenomicRanges? Michael Lawrence as.character method for GenomicRanges? Hervé Pagès as.character method for GenomicRanges? Nicolas Delhomme seqnames as a candidate for BiocGenerics Michael Lawrence seqnames as a candidate for BiocGenerics Hervé Pagès seqnames as a candidate for BiocGenerics Le Quan Ly unsubcribe

Sunday, April 26, 2015 5 emails

Henrik Bengtsson Bioc package pages: List also BugReports for a package? Sean Davis Just for fun Martin Morgan Biostring Nicolas Delhomme seqnames as a candidate for BiocGenerics a_kinga at yahoo.com Biostring

Saturday, April 25, 2015 1 email

Henrik Bengtsson Biobase: Imports repeats Depends

Friday, April 24, 2015 18 emails

Thursday, April 23, 2015 7 emails

Michael Lawrence Interoperability between DataFrame and dplyr? Ryan Interoperability between DataFrame and dplyr? Michael Lawrence Interoperability between DataFrame and dplyr? Vincent Carey Interoperability between DataFrame and dplyr? Ryan Interoperability between DataFrame and dplyr? Martin Morgan BioC 2015 Bioconductor Annual Conference Alessandro Mammana New-package: bamsignals

Wednesday, April 22, 2015 8 emails

Michael Lawrence mapping variadic calls to binary calls for dispatch Kasper Daniel Hansen build error, piano package Martin Morgan Append/combine option for filterFastq and similar? Ryan Append/combine option for filterFastq and similar? Jim Hester Append/combine option for filterFastq and similar? Ryan Append/combine option for filterFastq and similar? Dan Tenenbaum build error, piano package Aedin Culhane Append/combine option for filterFastq and similar?

Tuesday, April 21, 2015 8 emails

Leif Väremo build error, piano package Martin Morgan Append/combine option for filterFastq and similar? Ryan Append/combine option for filterFastq and similar? Kasper Daniel Hansen Use of confounders in downstream analysis Aileen Bahl Use of confounders in downstream analysis Hervé Pagès Error on Windows when selecting a single chromosome from a BSgenome Sean Davis Use of confounders in downstream analysis Aileen Bahl Use of confounders in downstream analysis

Monday, April 20, 2015 7 emails

Hervé Pagès coverage(gr, weight='score') does not work when score(gr) is an Rle Leonard Goldstein scanBam() segfault error Dan Tenenbaum today's devel build report Leonardo Collado Torres R 3.3 for snow leopard Dan Tenenbaum R 3.3 for snow leopard Dan Tenenbaum R 3.3 for snow leopard Martin Morgan scanBam() segfault error

Saturday, April 18, 2015 2 emails

Henrik Bengtsson Dependency issue Henrik Bengtsson Dependency issue

Friday, April 17, 2015 26 emails

Dan Tenenbaum Dependency issue t.kuilman at nki.nl Dependency issue Michael Lawrence coverage(gr, weight='score') does not work when score(gr) is an Rle Sergei Ryazansky Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Nicolas Delhomme R 3.3 for snow leopard Dan Tenenbaum Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Dan Tenenbaum Bioconductor 3.1 is released! Sergei Ryazansky Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Dan Tenenbaum Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Peter Haverty Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Sergei Ryazansky Error after upgrading to R 3.2.0 with loading of GO.db: 2 arguments passed to .Internal(ls) which requires 3 Dan Tenenbaum R 3.3 for snow leopard Leonardo Collado Torres R 3.3 for snow leopard Hervé Pagès coverage(gr, weight='score') does not work when score(gr) is an Rle Michael Lawrence coverage(gr, weight='score') does not work when score(gr) is an Rle Hervé Pagès coverage(gr, weight='score') does not work when score(gr) is an Rle Martin Morgan scanBam() segfault error Michael Lawrence coverage(gr, weight='score') does not work when score(gr) is an Rle Leonard Goldstein scanBam() segfault error Philip Lijnzaad coverage(gr, weight='score') does not work when score(gr) is an Rle Dan Tenenbaum BioC 3.1 branch created Thomas Maurel AnnotationHubData Error: Access denied: 530 Martin Morgan AnnotationHubData Error: Access denied: 530 Martin, Tiphaine BioC 3.1 branch created Kevin Rue-Albrecht BioC 3.1 branch created Martin, Tiphaine BioC 3.1 branch created

Thursday, April 16, 2015 8 emails

Henrik Bengtsson BioC 3.1 branch created Martin Morgan Update GSEABase to support new MSigDB collection in v5.0 Dan Tenenbaum BioC 3.1 branch created Henrik Bengtsson BioC 3.1 branch created Steve Lianoglou Update GSEABase to support new MSigDB collection in v5.0 Arora, Sonali AnnotationHubData Error: Access denied: 530 Dan Tenenbaum BioC 3.1 branch created Dan Tenenbaum Important: Bioconductor 3.1 branch to be created today - do not commit during this time

Wednesday, April 15, 2015 3 emails

Kasper Daniel Hansen request for more notices about build issues Dan Tenenbaum Docker granularity: containers for individual R packages, running on a normal R installation? Bastian Schiffthaler Docker granularity: containers for individual R packages, running on a normal R installation?

Tuesday, April 14, 2015 8 emails

Martin Morgan Docker granularity: containers for individual R packages, running on a normal R installation? Michael Lawrence Docker granularity: containers for individual R packages, running on a normal R installation? Wolfgang Huber Docker granularity: containers for individual R packages, running on a normal R installation? Nathaniel Hayden Proposed biocViews for Hi-C assay Michael Love request for more notices about build issues Dan Tenenbaum request for more notices about build issues Sean Davis Docker granularity: containers for individual R packages, running on a normal R installation? Wolfgang Huber Docker granularity: containers for individual R packages, running on a normal R installation?

Monday, April 13, 2015 6 emails

Dan Tenenbaum OpenMP on Mac OS "Mavericks" build server morelia Ulrich Bodenhofer OpenMP on Mac OS "Mavericks" build server morelia Marc Carlson AnnotationHubData Error: Access denied: 530 Dan Tenenbaum OpenMP on Mac OS "Mavericks" build server morelia Ulrich Bodenhofer OpenMP on Mac OS "Mavericks" build server morelia Thomas Maurel AnnotationHubData Error: Access denied: 530

Saturday, April 11, 2015 3 emails

Hervé Pagès Suggestion: export function fetchChromLengthsFromEnsembl in GenomicFeatures Rainer Johannes Suggestion: export function fetchChromLengthsFromEnsembl in GenomicFeatures Rainer Johannes AnnotationHubData Error: Access denied: 530

Friday, April 10, 2015 27 emails

Thursday, April 9, 2015 14 emails

Yu, Guangchuang Announcing a new package: ggtree Rainer Johannes AnnotationHubData Error: Access denied: 530 Djekidel Mohamed Nadhir Announcing a new package: R3CPET t.kuilman at nki.nl New package for copy number detection from targeted sequencing using off-target reads Dan Tenenbaum Disabling commits to release today; Update NEWS files, biocViews Nathaniel Hayden Proposed biocViews for Hi-C assay Martin Morgan AnnotationHub: ExpressionSetResource Error in Docker devel_core Ludwig Geistlinger AnnotationHub: ExpressionSetResource Error in Docker devel_core Vincent Carey AnnotationHub: ExpressionSetResource Error in Docker devel_core Josef Spidlen Announcing a new package: FlowRepositoryR Ludwig Geistlinger AnnotationHub: ExpressionSetResource Error in Docker devel_core Ludwig Geistlinger AnnotationHub: Error in Docker release_core Elena Grassi AnnotationHub: Error in Docker release_core Ludwig Geistlinger AnnotationHub: Error in Docker release_core

Wednesday, April 8, 2015 5 emails

Hervé Pagès New package: coMET Sean Davis request for more notices about build issues Dan Tenenbaum request for more notices about build issues Michael Love request for more notices about build issues Radu Zabet Announcing a new package: DMRcaller

Monday, April 6, 2015 10 emails

Tim Triche, Jr. BrowserViz and sub-protocols Tim Triche, Jr. BrowserViz and sub-protocols Michael Lawrence BrowserViz and sub-protocols Dan Tenenbaum BrowserViz and sub-protocols Michael Lawrence BrowserViz and sub-protocols Jesper Gådin SummarizedExperiment subset of 4 dimensions Leonardo Collado Torres recalling methods Tim Triche, Jr. BrowserViz and sub-protocols Michael Lawrence BrowserViz and sub-protocols Michael Love recalling methods

Friday, April 3, 2015 11 emails

Hector Corrada Bravo BrowserViz Michael Lawrence BrowserViz Michael Lawrence BrowserViz Leonardo Collado Torres BrowserViz: curious but needs a small tweak to run example Michael Lawrence BrowserViz Valerie Obenchain Bioconductor Newsletter - April 2015 Martin Morgan Build error for DESeq2 dev causing error in other package builds Michael Love Build error for DESeq2 dev causing error in other package builds Andrea Rau Build error for DESeq2 dev causing error in other package builds Michael Love SummarizedExperiment, differing assay dimnames Michael Love SummarizedExperiment, differing assay dimnames

Thursday, April 2, 2015 2 emails

Michael Lawrence issue about S4 slot has a dist object. Bernat Gel Announcing a new package: regioneR

Wednesday, April 1, 2015 16 emails

Bioc-devel April 2015