Bioc-devel December 2015

Error in NSBS

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4 msgs · Dec 10 – Dec 11

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Krithika Bhuvaneshwar [kb472@georgetown.edu] Error in NSBS Dec 10, 2015

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Hervé Pagès Error in NSBS Dec 11, 2015

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Hervé Pagès Error in NSBS Dec 11, 2015

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Michael Lawrence Error in NSBS Dec 11, 2015

Extending biovizBase and ggbio packages

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12 msgs · Dec 14 – Dec 16

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Rainer Johannes Extending biovizBase and ggbio packages Dec 14, 2015

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Michael Lawrence Extending biovizBase and ggbio packages Dec 14, 2015

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Rainer Johannes Extending biovizBase and ggbio packages Dec 14, 2015

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Michael Lawrence Extending biovizBase and ggbio packages Dec 14, 2015

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Martin Morgan Extending biovizBase and ggbio packages Dec 14, 2015

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Jim Hester Extending biovizBase and ggbio packages Dec 14, 2015

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Rainer Johannes Extending biovizBase and ggbio packages Dec 14, 2015

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Rainer Johannes Extending biovizBase and ggbio packages Dec 15, 2015

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Michael Lawrence Extending biovizBase and ggbio packages Dec 15, 2015

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Rainer Johannes Extending biovizBase and ggbio packages Dec 15, 2015

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Rainer Johannes Extending biovizBase and ggbio packages Dec 16, 2015

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Michael Lawrence Extending biovizBase and ggbio packages Dec 16, 2015

For integer vectors, `as(x, "numeric")` has no effect.

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8 msgs · Dec 11 – Dec 26

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Martin Maechler For integer vectors, `as(x, "numeric")` has no effect. Dec 11, 2015

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John Chambers For integer vectors, `as(x, "numeric")` has no effect. Dec 11, 2015

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Martin Morgan For integer vectors, `as(x, "numeric")` has no effect. Dec 11, 2015

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Martin Maechler For integer vectors, `as(x, "numeric")` has no effect. Dec 12, 2015

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Martin Maechler For integer vectors, `as(x, "numeric")` has no effect. Dec 19, 2015

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John Chambers For integer vectors, `as(x, "numeric")` has no effect. Dec 19, 2015

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Hervé Pagès For integer vectors, `as(x, "numeric")` has no effect. Dec 25, 2015

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John Chambers For integer vectors, `as(x, "numeric")` has no effect. Dec 26, 2015

Git-Svn bridge will be removed permanently on January 29, 2016

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1 msg · Dec 28

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Dan Tenenbaum Git-Svn bridge will be removed permanently on January 29, 2016 Dec 28, 2015

Is there a way to change the name of R package that is already published on bioconductor?

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2 msgs · Dec 2 – Dec 7

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Hervé Pagès Is there a way to change the name of R package that is already published on bioconductor? Dec 2, 2015

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Marcin Kosiński Is there a way to change the name of R package that is already published on bioconductor? Dec 7, 2015

Issue with pushing git commits to SVN

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3 msgs · Dec 12 – Dec 13

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Federico Comoglio Issue with pushing git commits to SVN Dec 12, 2015

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Jim Hester Issue with pushing git commits to SVN Dec 13, 2015

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Federico Comoglio Issue with pushing git commits to SVN Dec 13, 2015

New instance types for Bioconductor AMI

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2 msgs · Dec 4 – Dec 4

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Thomas Lin Pedersen New instance types for Bioconductor AMI Dec 4, 2015

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Dan Tenenbaum New instance types for Bioconductor AMI Dec 4, 2015

New package: FamAgg - familial aggregation analysis in large pedigrees

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1 msg · Dec 1

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Rainer Johannes New package: FamAgg - familial aggregation analysis in large pedigrees Dec 1, 2015

Progress Message Order in bplapply

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4 msgs · Dec 27 – Dec 28

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Dario Strbenac Progress Message Order in bplapply Dec 27, 2015

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Dan Tenenbaum Progress Message Order in bplapply Dec 28, 2015

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Martin Morgan Progress Message Order in bplapply Dec 28, 2015

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Dario Strbenac Progress Message Order in bplapply Dec 28, 2015

R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

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1 msg · Dec 17

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Obenchain, Valerie R CMD SHLIB throwing error on zin1 (linux) BioC nightly build Dec 17, 2015

R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

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1 msg · Dec 14

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Martin Morgan R CMD SHLIB throwing error on zin1 (linux) BioC nightly build Dec 14, 2015

R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

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1 msg · Dec 14

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Dan Tenenbaum R CMD SHLIB throwing error on zin1 (linux) BioC nightly build Dec 14, 2015

R CMD SHLIB throwing error on zin1 (linux) BioC nightly build

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3 msgs · Dec 14 – Dec 17

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Brad Friedman R CMD SHLIB throwing error on zin1 (linux) BioC nightly build Dec 14, 2015

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Obenchain, Valerie R CMD SHLIB throwing error on zin1 (linux) BioC nightly build Dec 17, 2015

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Brad Friedman R CMD SHLIB throwing error on zin1 (linux) BioC nightly build Dec 17, 2015

Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’

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4 msgs · Dec 21 – Dec 21

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Arora, Sonali Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’ Dec 21, 2015

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Martin Morgan Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’ Dec 21, 2015

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Arora, Sonali Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’ Dec 21, 2015

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Martin Morgan Rsamtools/AnnotationHub Error for FaFile - multiple methods tables found for ‘relistToClass’ Dec 21, 2015

Test coverage for packages not calculated/updated?

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1 msg · Dec 4

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Rainer Johannes Test coverage for packages not calculated/updated? Dec 4, 2015

Tracing a build error on moscato2: could it be that pandoc is not updated?

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1 msg · Dec 4

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Dan Tenenbaum Tracing a build error on moscato2: could it be that pandoc is not updated? Dec 4, 2015

Tracing a build error on moscato2: could it be that pandoc is not updated?

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1 msg · Dec 2

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Leonardo Collado Torres Tracing a build error on moscato2: could it be that pandoc is not updated? Dec 2, 2015

Unexpected behaviour with Assays and Vector classes

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1 msg · Dec 3

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Martin Morgan Unexpected behaviour with Assays and Vector classes Dec 3, 2015

Warning: no visible global function definition for ‘seqlevels<-’

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2 msgs · Dec 22 – Dec 22

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Venkat Malladi Warning: no visible global function definition for ‘seqlevels<-’ Dec 22, 2015

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Martin Morgan Warning: no visible global function definition for ‘seqlevels<-’ Dec 22, 2015

as.table not available for HitsList anymore?

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3 msgs · Dec 20 – Dec 20

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Nicolas Delhomme as.table not available for HitsList anymore? Dec 20, 2015

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Martin Morgan as.table not available for HitsList anymore? Dec 20, 2015

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Nicolas Delhomme as.table not available for HitsList anymore? Dec 20, 2015

bioconductor.org scheduled downtime, Thursday, December 31st, 12:01PM PST

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1 msg · Dec 28

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Dan Tenenbaum bioconductor.org scheduled downtime, Thursday, December 31st, 12:01PM PST Dec 28, 2015

bplapply Processes Sometimes Stall

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4 msgs · Dec 27 – Dec 29

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Dario Strbenac bplapply Processes Sometimes Stall Dec 27, 2015

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Martin Morgan bplapply Processes Sometimes Stall Dec 28, 2015

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Dario Strbenac bplapply Processes Sometimes Stall Dec 28, 2015

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Dario Strbenac bplapply Processes Sometimes Stall Dec 29, 2015

do SummarizedExperiments really need colnames?

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5 msgs · Dec 5 – Dec 13

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Aaron Lun do SummarizedExperiments really need colnames? Dec 5, 2015

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Martin Morgan do SummarizedExperiments really need colnames? Dec 5, 2015

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Aaron Lun do SummarizedExperiments really need colnames? Dec 5, 2015

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Peter Hickey do SummarizedExperiments really need colnames? Dec 6, 2015

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Martin Morgan do SummarizedExperiments really need colnames? Dec 13, 2015

error when combining objects inheriting from GRangesList

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3 msgs · Dec 4 – Dec 4

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Leonard Goldstein error when combining objects inheriting from GRangesList Dec 4, 2015

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Hervé Pagès error when combining objects inheriting from GRangesList Dec 4, 2015

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Leonard Goldstein error when combining objects inheriting from GRangesList Dec 4, 2015

ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position?

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4 msgs · Dec 19 – Dec 19

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Lorena Pantano ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position? Dec 19, 2015

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Martin Morgan ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position? Dec 19, 2015

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Martin Morgan ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position? Dec 19, 2015

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Michael Love ggplot2 2.0.0 export Position now, conflict with BiocGeneric::Position? Dec 19, 2015

git svn trouble on release branch

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4 msgs · Dec 18 – Dec 18

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Kyle Bemis git svn trouble on release branch Dec 18, 2015

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Leonardo Collado Torres git svn trouble on release branch Dec 18, 2015

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Jim Hester git svn trouble on release branch Dec 18, 2015

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Jim Hester git svn trouble on release branch Dec 18, 2015

include .DollarNames.ExpressionSet in Biobase?

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3 msgs · Dec 4 – Dec 4

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Angerer, Philipp include .DollarNames.ExpressionSet in Biobase? Dec 4, 2015

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Martin Morgan include .DollarNames.ExpressionSet in Biobase? Dec 4, 2015

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Martin Morgan include .DollarNames.ExpressionSet in Biobase? Dec 4, 2015

mapIds methods for ExpressionSet and SummarizedExperiment

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1 msg · Dec 18

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Martin Morgan mapIds methods for ExpressionSet and SummarizedExperiment Dec 18, 2015

mapIds methods for ExpressionSet and SummarizedExperiment

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1 msg · Dec 18

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Martin Morgan mapIds methods for ExpressionSet and SummarizedExperiment Dec 18, 2015

mapIds methods for ExpressionSet and SummarizedExperiment

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2 msgs · Dec 17 – Dec 21

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Ludwig Geistlinger mapIds methods for ExpressionSet and SummarizedExperiment Dec 17, 2015

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Ludwig Geistlinger mapIds methods for ExpressionSet and SummarizedExperiment Dec 21, 2015

namespace GenomicRanges

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2 msgs · Dec 2 – Dec 2

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Karl Stamm namespace GenomicRanges Dec 2, 2015

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Hervé Pagès namespace GenomicRanges Dec 2, 2015

ncdf deprecation

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2 msgs · Dec 1 – Dec 4

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Hervé Pagès ncdf deprecation Dec 1, 2015

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Dan Tenenbaum ncdf deprecation Dec 4, 2015

segfault when using RleList in DataFrames

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4 msgs · Dec 5 – Dec 7

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Leonard Goldstein segfault when using RleList in DataFrames Dec 5, 2015

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Peter Hickey segfault when using RleList in DataFrames Dec 6, 2015

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Hervé Pagès segfault when using RleList in DataFrames Dec 7, 2015

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Leonard Goldstein segfault when using RleList in DataFrames Dec 7, 2015

seqlevelsStyle on alternate chromosomes

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5 msgs · Dec 17 – Dec 21

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Michael Lawrence seqlevelsStyle on alternate chromosomes Dec 17, 2015

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Hervé Pagès seqlevelsStyle on alternate chromosomes Dec 17, 2015

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Leonardo Collado Torres seqlevelsStyle on alternate chromosomes Dec 17, 2015

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Michael Lawrence seqlevelsStyle on alternate chromosomes Dec 18, 2015

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Arora, Sonali seqlevelsStyle on alternate chromosomes Dec 21, 2015

strange bug in a BioC workflow that only appears on Jenkis

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2 msgs · Dec 4 – Dec 7

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Dan Tenenbaum strange bug in a BioC workflow that only appears on Jenkis Dec 4, 2015

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Bernd Klaus strange bug in a BioC workflow that only appears on Jenkis Dec 7, 2015

strange bug in a BioC workflow that only appears on Jenkis

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2 msgs · Dec 3 – Dec 14

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Bernd Klaus strange bug in a BioC workflow that only appears on Jenkis Dec 3, 2015

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Bernd Klaus strange bug in a BioC workflow that only appears on Jenkis Dec 14, 2015

summarizeOverlaps provide a non existing algorithm argument to findOverlaps

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3 msgs · Dec 21 – Dec 26

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Nicolas Delhomme summarizeOverlaps provide a non existing algorithm argument to findOverlaps Dec 21, 2015

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Hervé Pagès summarizeOverlaps provide a non existing algorithm argument to findOverlaps Dec 25, 2015

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Nicolas Delhomme summarizeOverlaps provide a non existing algorithm argument to findOverlaps Dec 26, 2015

support for BEDPE import/export in rtracklayer?

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2 msgs · Dec 8 – Dec 8

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Aaron Lun support for BEDPE import/export in rtracklayer? Dec 8, 2015

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Michael Lawrence support for BEDPE import/export in rtracklayer? Dec 8, 2015

systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

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4 msgs · Dec 1 – Dec 2

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Cook, Malcolm systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : Dec 1, 2015

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Hervé Pagès systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : Dec 1, 2015

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Thomas Girke systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : Dec 1, 2015

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Hervé Pagès systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : Dec 2, 2015

what is SummarizedExperiment a Vector of?

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7 msgs · Dec 15 – Dec 15

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Michael Lawrence what is SummarizedExperiment a Vector of? Dec 15, 2015

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Vincent Carey what is SummarizedExperiment a Vector of? Dec 15, 2015

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Michael Lawrence what is SummarizedExperiment a Vector of? Dec 15, 2015

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Vincent Carey what is SummarizedExperiment a Vector of? Dec 15, 2015

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Hervé Pagès what is SummarizedExperiment a Vector of? Dec 15, 2015

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Michael Lawrence what is SummarizedExperiment a Vector of? Dec 15, 2015

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Hervé Pagès what is SummarizedExperiment a Vector of? Dec 15, 2015

winbuilder1 in the workflow CI system offline ...

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4 msgs · Dec 2 – Dec 3

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Bernd Klaus winbuilder1 in the workflow CI system offline ... Dec 2, 2015

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Brian Long winbuilder1 in the workflow CI system offline ... Dec 2, 2015

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Brian Long winbuilder1 in the workflow CI system offline ... Dec 2, 2015

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Bernd Klaus winbuilder1 in the workflow CI system offline ... Dec 3, 2015