Bioc-devel - October 2016 - Thread View

[Bioc-devel] BiocInstaller fails to load with older R if messages suppressed

2 msgs Oct 31

Kevin Ushey BiocInstaller fails to load with older R if messages suppressed Oct 31, 2016

Martin Morgan BiocInstaller fails to load with older R if messages suppressed Oct 31, 2016

[Bioc-devel] compiler package

2 msgs Oct 30

Ioannis Vardaxis compiler package Oct 30, 2016

Vincent Carey compiler package Oct 30, 2016

[Bioc-devel] Fwd: Question about a package submission

12 msgs Oct 28

Ioannis Vardaxis Question about a package submission Oct 25, 2016

Ioannis Vardaxis Question about a package submission Oct 27, 2016

Vincent Carey Question about a package submission Oct 27, 2016

Kevin RUE Question about a package submission Oct 27, 2016

Martin Morgan Question about a package submission Oct 27, 2016

Kevin RUE Question about a package submission Oct 28, 2016

Ioannis Vardaxis Question about a package submission Oct 28, 2016

Kevin RUE Question about a package submission Oct 28, 2016

Martin Morgan Question about a package submission Oct 28, 2016

[Bioc-devel] lumi package is not available

1 msg Oct 28

Gang Feng lumi package is not available Oct 28, 2016

[Bioc-devel] lumi package is not available

2 msgs Oct 28

王棣台 lumi package is not available Oct 28, 2016

Kevin RUE lumi package is not available Oct 28, 2016

[Bioc-devel] Subversion server "hedgehog" reboot Thursday 10/27 4:00 PM Seattle time

1 msg Oct 27

Hervé Pagès Subversion server "hedgehog" reboot Thursday 10/27 4:00 PM Seattle time Oct 27, 2016

[Bioc-devel] incomplete vignette on macosx

2 msgs Oct 27

Hervé Pagès incomplete vignette on macosx Oct 26, 2016

Renan Valieris incomplete vignette on macosx Oct 27, 2016

[Bioc-devel] Fwd: Question about a package submission

1 msg Oct 27

Vincent Carey Question about a package submission Oct 27, 2016

[Bioc-devel] RankProd (development) - install and build error in oaxaca

1 msg Oct 26

Hervé Pagès RankProd (development) - install and build error in oaxaca Oct 26, 2016

[Bioc-devel] Build OK in devel, Mac OS error in release (CausalR)

2 msgs Oct 26

Glyn Bradley Build OK in devel, Mac OS error in release (CausalR) Oct 26, 2016

Hervé Pagès Build OK in devel, Mac OS error in release (CausalR) Oct 26, 2016

[Bioc-devel] Build error: Dependency 'Biobase' is not available

2 msgs Oct 26

Hervé Pagès Build error: Dependency 'Biobase' is not available Oct 26, 2016

Shraddha Pai Build error: Dependency 'Biobase' is not available Oct 26, 2016

[Bioc-devel] Build error: Dependency 'Biobase' is not available

1 msg Oct 26

Shraddha Pai Build error: Dependency 'Biobase' is not available Oct 26, 2016

[Bioc-devel] ignoreSelf Option for findOverlaps of GenomicRanges Query

4 msgs Oct 26

Dario Strbenac ignoreSelf Option for findOverlaps of GenomicRanges Query Oct 26, 2016

Michael Lawrence ignoreSelf Option for findOverlaps of GenomicRanges Query Oct 26, 2016

Hervé Pagès ignoreSelf Option for findOverlaps of GenomicRanges Query Oct 26, 2016

[Bioc-devel] RankProd (development) - install and build error in oaxaca

2 msgs Oct 26

Francesco Del Carratore RankProd (development) - install and build error in oaxaca Oct 26, 2016

Pedro Madrigal RankProd (development) - install and build error in oaxaca Oct 26, 2016

[Bioc-devel] incomplete vignette on macosx

1 msg Oct 25

Renan Valieris incomplete vignette on macosx Oct 25, 2016

[Bioc-devel] No release svn repository for proFIA/plasFIA maintainer

1 msg Oct 25

Dan Tenenbaum No release svn repository for proFIA/plasFIA maintainer Oct 25, 2016

[Bioc-devel] svn repository for proFIA/plasFIA maintainer

1 msg Oct 25

Obenchain, Valerie svn repository for proFIA/plasFIA maintainer Oct 25, 2016

[Bioc-devel] Error in DESeq Installation

2 msgs Oct 25

Yogesh Gupta Error in DESeq Installation Oct 23, 2016

Obenchain, Valerie Error in DESeq Installation Oct 25, 2016

[Bioc-devel] No release svn repository for proFIA/plasFIA maintainer

1 msg Oct 25

DELABRIÈRE Alexis No release svn repository for proFIA/plasFIA maintainer Oct 25, 2016

[Bioc-devel] SummarizedExperiment

3 msgs Oct 24

Rodriguez Martinez, Andrea SummarizedExperiment Oct 24, 2016

Martin Morgan SummarizedExperiment Oct 24, 2016

Rodriguez Martinez, Andrea SummarizedExperiment Oct 24, 2016

[Bioc-devel] odd svn event

2 msgs Oct 24

Vincent Carey odd svn event Oct 23, 2016

Andrzej Oleś odd svn event Oct 24, 2016

[Bioc-devel] Author names with special characters

3 msgs Oct 23

Nuno Agostinho Author names with special characters Oct 23, 2016

Neumann, Steffen Author names with special characters Oct 23, 2016

Nuno Agostinho Author names with special characters Oct 23, 2016

[Bioc-devel] Question about InteractionSet package

2 msgs Oct 21

Dan Tenenbaum Question about InteractionSet package Oct 21, 2016

[Bioc-devel] Question about InteractionSet package

1 msg Oct 21

Ioannis Vardaxis Question about InteractionSet package Oct 21, 2016

[Bioc-devel] Submitted package not available in Bioconductor 3.4

3 msgs Oct 21

Andreas Kapouranis Submitted package not available in Bioconductor 3.4 Oct 21, 2016

Martin Morgan Submitted package not available in Bioconductor 3.4 Oct 21, 2016

Andreas Kapouranis Submitted package not available in Bioconductor 3.4 Oct 21, 2016

[Bioc-devel] Fwd: BiocInstaller::useDevel() Error: 'devel' version requires a more recent R

13 msgs Oct 20

Michael Lawrence BiocInstaller::useDevel() Error: 'devel' version requires a more recent R Oct 19, 2016

Martin Morgan BiocInstaller::useDevel() Error: 'devel' version requires a more recent R Oct 20, 2016

Rodriguez Martinez, Andrea BiocInstaller::useDevel() Error: 'devel' version requires a more recent R Oct 20, 2016

Martin Morgan BiocInstaller::useDevel() Error: 'devel' version requires a more recent R Oct 20, 2016

Kevin RUE BiocInstaller::useDevel() Error: 'devel' version requires a more recent R Oct 20, 2016

Lukas Weber BiocInstaller::useDevel() Error: 'devel' version requires a more recent R Oct 20, 2016

Kevin RUE BiocInstaller::useDevel() Error: 'devel' version requires a more recent R Oct 20, 2016

Kasper Daniel Hansen BiocInstaller::useDevel() Error: 'devel' version requires a more recent R Oct 20, 2016

Lukas Weber BiocInstaller::useDevel() Error: 'devel' version requires a more recent R Oct 20, 2016

Rodriguez Martinez, Andrea BiocInstaller::useDevel() Error: 'devel' version requires a more recent R Oct 20, 2016

[Bioc-devel] Doubt with deprecating a function

2 msgs Oct 20

Carlos Ruiz Doubt with deprecating a function Oct 19, 2016

Obenchain, Valerie Doubt with deprecating a function Oct 20, 2016

[Bioc-devel] BiocInstaller::useDevel() Error: 'devel' version requires a more recent R

2 msgs Oct 19

Rodriguez Martinez, Andrea BiocInstaller::useDevel() Error: 'devel' version requires a more recent R Oct 19, 2016

Michael Lawrence BiocInstaller::useDevel() Error: 'devel' version requires a more recent R Oct 19, 2016

[Bioc-devel] Package "not supported" on some platforms, and dependent packages

4 msgs Oct 19

Dan Tenenbaum Package "not supported" on some platforms, and dependent packages Oct 18, 2016

Kevin RUE Package "not supported" on some platforms, and dependent packages Oct 18, 2016

Obenchain, Valerie Package "not supported" on some platforms, and dependent packages Oct 19, 2016

Kevin RUE Package "not supported" on some platforms, and dependent packages Oct 19, 2016

[Bioc-devel] github-mirror of ensembldb out of sync with BioC svn

4 msgs Oct 19

Rainer Johannes github-mirror of ensembldb out of sync with BioC svn Oct 19, 2016

Leonardo Collado Torres github-mirror of ensembldb out of sync with BioC svn Oct 19, 2016

Martin Morgan github-mirror of ensembldb out of sync with BioC svn Oct 19, 2016

Leonardo Collado Torres github-mirror of ensembldb out of sync with BioC svn Oct 19, 2016

[Bioc-devel] Bioconductor 3.4 is released

3 msgs Oct 18

Hervé Pagès Bioconductor 3.4 is released Oct 18, 2016

Lorena Pantano Bioconductor 3.4 is released Oct 18, 2016

Martin Morgan Bioconductor 3.4 is released Oct 18, 2016

[Bioc-devel] staging.bioconductor.org not responsive

3 msgs Oct 18

Martin Morgan staging.bioconductor.org not responsive Oct 18, 2016

Dan Tenenbaum staging.bioconductor.org not responsive Oct 18, 2016

Martin Morgan staging.bioconductor.org not responsive Oct 18, 2016

[Bioc-devel] Package "not supported" on some platforms, and dependent packages

1 msg Oct 18

Kevin RUE Package "not supported" on some platforms, and dependent packages Oct 18, 2016

[Bioc-devel] Ascona Workshop 2017: Call for abstracts

1 msg Oct 18

Wolfgang Huber Ascona Workshop 2017: Call for abstracts Oct 18, 2016

[Bioc-devel] BioC 3.4: several package failures traceable to vsn req. R >= 3.4.0?

2 msgs Oct 17

Hervé Pagès BioC 3.4: several package failures traceable to vsn req. R >= 3.4.0? Oct 17, 2016

Ramon Diaz-Uriarte BioC 3.4: several package failures traceable to vsn req. R >= 3.4.0? Oct 17, 2016

[Bioc-devel] 3.4 branch created in svn

1 msg Oct 17

Hervé Pagès 3.4 branch created in svn Oct 17, 2016

[Bioc-devel] Bioconductor 3.4 branch to be created in about 1 hour - do not commit during this time

1 msg Oct 17

Hervé Pagès Bioconductor 3.4 branch to be created in about 1 hour - do not commit during this time Oct 17, 2016

[Bioc-devel] A bug in TxDb.Hsapiens.UCSC.hg38.knownGene?

2 msgs Oct 17

Hervé Pagès A bug in TxDb.Hsapiens.UCSC.hg38.knownGene? Oct 17, 2016

zhao shilin A bug in TxDb.Hsapiens.UCSC.hg38.knownGene? Oct 17, 2016

[Bioc-devel] BioC 3.4: several package failures traceable to vsn req. R >= 3.4.0?

2 msgs Oct 17

Ramon Diaz-Uriarte BioC 3.4: several package failures traceable to vsn req. R >= 3.4.0? Oct 17, 2016

Panagiotis Moulos BioC 3.4: several package failures traceable to vsn req. R >= 3.4.0? Oct 17, 2016

[Bioc-devel] A bug in TxDb.Hsapiens.UCSC.hg38.knownGene?

1 msg Oct 16

zhao shilin A bug in TxDb.Hsapiens.UCSC.hg38.knownGene? Oct 16, 2016

[Bioc-devel] GitHub and svn

6 msgs Oct 16

Gabriel Becker GitHub and svn Oct 15, 2016

S Manimaran GitHub and svn Oct 15, 2016

Kevin RUE GitHub and svn Oct 15, 2016

Nathan Sheffield GitHub and svn Oct 15, 2016

Henrik Bengtsson GitHub and svn Oct 15, 2016

S Manimaran GitHub and svn Oct 16, 2016

[Bioc-devel] Version on GitHub mirror different than Bioconductor

4 msgs Oct 16

Raymond Cavalcante Version on GitHub mirror different than Bioconductor Oct 15, 2016

Martin Morgan Version on GitHub mirror different than Bioconductor Oct 15, 2016

Raymond Cavalcante Version on GitHub mirror different than Bioconductor Oct 15, 2016

Martin Morgan Version on GitHub mirror different than Bioconductor Oct 16, 2016

[Bioc-devel] GitHub and svn

2 msgs Oct 15

S Manimaran GitHub and svn Oct 15, 2016

Kasper Daniel Hansen GitHub and svn Oct 15, 2016

[Bioc-devel] SVN repo and git mirror for accepted package

4 msgs Oct 15

Lukas Weber SVN repo and git mirror for accepted package Oct 15, 2016

Martin Morgan SVN repo and git mirror for accepted package Oct 15, 2016

Lukas Weber SVN repo and git mirror for accepted package Oct 15, 2016

Marcel Ramos SVN repo and git mirror for accepted package Oct 15, 2016

[Bioc-devel] Build failure for new package

3 msgs Oct 14

Tyler Smith Build failure for new package Oct 14, 2016

Martin Morgan Build failure for new package Oct 14, 2016

[Bioc-devel] biocLite() repository not available for Bioconductor 3.4

2 msgs Oct 14

Martin Morgan biocLite() repository not available for Bioconductor 3.4 Oct 14, 2016

Hervé Pagès biocLite() repository not available for Bioconductor 3.4 Oct 14, 2016

[Bioc-devel] Need help

2 msgs Oct 14

Arvind Korwar Need help Oct 14, 2016

Laurent Gatto Need help Oct 14, 2016

[Bioc-devel] biocLite and useDevel

1 msg Oct 14

Dan Tenenbaum biocLite and useDevel Oct 14, 2016

[Bioc-devel] biocLite and useDevel

1 msg Oct 14

Kasper Daniel Hansen biocLite and useDevel Oct 14, 2016

[Bioc-devel] maftools build error

2 msgs Oct 14

Anand MT maftools build error Oct 9, 2016

Obenchain, Valerie maftools build error Oct 14, 2016

[Bioc-devel] msPurity check failure on Windows

5 msgs Oct 14

Thomas Lawson msPurity check failure on Windows Oct 13, 2016

Martin Morgan msPurity check failure on Windows Oct 13, 2016

Thomas Lawson msPurity check failure on Windows Oct 13, 2016

Thomas Lawson msPurity check failure on Windows Oct 14, 2016

Martin Morgan msPurity check failure on Windows Oct 14, 2016

[Bioc-devel] RMassBank (almost) builds ...

1 msg Oct 13

Stravs, Michael RMassBank (almost) builds ... Oct 13, 2016

[Bioc-devel] RMassBank (almost) builds ...

1 msg Oct 13

Egon Willighagen RMassBank (almost) builds ... Oct 13, 2016

[Bioc-devel] RMassBank (almost) builds ...

3 msgs Oct 13

Schymanski, Emma RMassBank (almost) builds ... Oct 12, 2016

Egon Willighagen RMassBank (almost) builds ... Oct 13, 2016

Hervé Pagès RMassBank (almost) builds ... Oct 13, 2016

[Bioc-devel] NEWS files

5 msgs Oct 12

Martin Morgan NEWS files Oct 12, 2016

Dario Strbenac NEWS files Oct 12, 2016

Hervé Pagès NEWS files Oct 12, 2016

Martin Morgan NEWS files Oct 12, 2016

Dario Strbenac NEWS files Oct 12, 2016

[Bioc-devel] Automatic build failure notifications

4 msgs Oct 12

Schymanski, Emma Automatic build failure notifications Oct 10, 2016

Hervé Pagès Automatic build failure notifications Oct 11, 2016

Dan Tenenbaum Automatic build failure notifications Oct 11, 2016

Hervé Pagès Automatic build failure notifications Oct 12, 2016

[Bioc-devel] Release branch commits disabled today

2 msgs Oct 12

Martin Morgan Release branch commits disabled today Oct 12, 2016

[Bioc-devel] philr recent build fail

2 msgs Oct 12

Justin Silverman philr recent build fail Oct 12, 2016

Shepherd, Lori philr recent build fail Oct 12, 2016

[Bioc-devel] flowCore fails with GCC 4.4.7 on RHEL 6.0

6 msgs Oct 11

Kasper Daniel Hansen flowCore fails with GCC 4.4.7 on RHEL 6.0 Oct 10, 2016

Mike flowCore fails with GCC 4.4.7 on RHEL 6.0 Oct 11, 2016

Kasper Daniel Hansen flowCore fails with GCC 4.4.7 on RHEL 6.0 Oct 11, 2016

Dan Tenenbaum flowCore fails with GCC 4.4.7 on RHEL 6.0 Oct 11, 2016

Kasper Daniel Hansen flowCore fails with GCC 4.4.7 on RHEL 6.0 Oct 11, 2016

Henrik Bengtsson flowCore fails with GCC 4.4.7 on RHEL 6.0 Oct 11, 2016

[Bioc-devel] Handling of classVersion

1 msg Oct 11

Laurent Gatto Handling of classVersion Oct 11, 2016

[Bioc-devel] DeepBlueR check error

1 msg Oct 10

Hervé Pagès DeepBlueR check error Oct 10, 2016

[Bioc-devel] DeepBlueR check error

1 msg Oct 10

Markus List DeepBlueR check error Oct 10, 2016

[Bioc-devel] RMassBank build error

8 msgs Oct 10

Rainer Johannes RMassBank build error Oct 7, 2016

Laurent Gatto RMassBank build error Oct 7, 2016

Stravs, Michael RMassBank build error Oct 9, 2016

Laurent Gatto RMassBank build error Oct 9, 2016

Kasper Daniel Hansen RMassBank build error Oct 9, 2016

Stravs, Michael RMassBank build error Oct 10, 2016

Rainer Johannes RMassBank build error Oct 10, 2016

Laurent Gatto RMassBank build error Oct 10, 2016

[Bioc-devel] Harman not building on Windows due to mzR

8 msgs Oct 9

Hervé Pagès Harman not building on Windows due to mzR Oct 5, 2016

Neumann, Steffen Harman not building on Windows due to mzR Oct 6, 2016

Hervé Pagès Harman not building on Windows due to mzR Oct 6, 2016

Laurent Gatto Harman not building on Windows due to mzR Oct 6, 2016

Hervé Pagès Harman not building on Windows due to mzR Oct 6, 2016

Jason.Ross at csiro.au Harman not building on Windows due to mzR Oct 6, 2016

Neumann, Steffen Harman not building on Windows due to mzR Oct 7, 2016

Neumann, Steffen Harman not building on Windows due to mzR Oct 9, 2016

[Bioc-devel] tokay1 building error

1 msg Oct 8

Hervé Pagès tokay1 building error Oct 8, 2016

[Bioc-devel] patch for isobar package

3 msgs Oct 8

Laurent Gatto patch for isobar package Oct 7, 2016

Martin Morgan patch for isobar package Oct 8, 2016

Florian Breitwieser patch for isobar package Oct 8, 2016

[Bioc-devel] RMassBank build error

4 msgs Oct 8

Schymanski, Emma RMassBank build error Oct 7, 2016

Obenchain, Valerie RMassBank build error Oct 7, 2016

Laurent Gatto RMassBank build error Oct 7, 2016

Martin Morgan RMassBank build error Oct 8, 2016

[Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

7 msgs Oct 7

Hervé Pagès tokay1 (windows) build server cannot use the nbconvertR vignette engine Oct 4, 2016

Andrzej Oleś tokay1 (windows) build server cannot use the nbconvertR vignette engine Oct 4, 2016

Dan Tenenbaum tokay1 (windows) build server cannot use the nbconvertR vignette engine Oct 4, 2016

Hervé Pagès tokay1 (windows) build server cannot use the nbconvertR vignette engine Oct 4, 2016

Dan Tenenbaum tokay1 (windows) build server cannot use the nbconvertR vignette engine Oct 4, 2016

Angerer, Philipp tokay1 (windows) build server cannot use the nbconvertR vignette engine Oct 5, 2016

Hervé Pagès tokay1 (windows) build server cannot use the nbconvertR vignette engine Oct 7, 2016

[Bioc-devel] tokay1 building error

1 msg Oct 7

Wachter, Astrid tokay1 building error Oct 7, 2016

[Bioc-devel] Bioconductor 3.4 release schedule

3 msgs Oct 7

Tyler Smith Bioconductor 3.4 release schedule Oct 5, 2016

Martin Morgan Bioconductor 3.4 release schedule Oct 5, 2016

Tyler Smith Bioconductor 3.4 release schedule Oct 7, 2016

[Bioc-devel] unable to install/download IRanges, Biobase, GenomeInfoDb

3 msgs Oct 6

Rodriguez Martinez, Andrea unable to install/download IRanges, Biobase, GenomeInfoDb Oct 6, 2016

Dan Tenenbaum unable to install/download IRanges, Biobase, GenomeInfoDb Oct 6, 2016

Rodriguez Martinez, Andrea unable to install/download IRanges, Biobase, GenomeInfoDb Oct 6, 2016

[Bioc-devel] Harman not building on Windows due to mzR

2 msgs Oct 6

Hervé Pagès Harman not building on Windows due to mzR Oct 5, 2016

Neumann, Steffen Harman not building on Windows due to mzR Oct 6, 2016

[Bioc-devel] Bioconductor 3.4 release schedule

2 msgs Oct 5

Kasper Daniel Hansen Bioconductor 3.4 release schedule Oct 5, 2016

Hervé Pagès Bioconductor 3.4 release schedule Oct 5, 2016

[Bioc-devel] warning on GenomeInfoDb::keepStandardChromosomes()

2 msgs Oct 5

Robert Castelo warning on GenomeInfoDb::keepStandardChromosomes() Oct 5, 2016

Shepherd, Lori warning on GenomeInfoDb::keepStandardChromosomes() Oct 5, 2016

[Bioc-devel] Why can't NAMESPACE be a strict subset of DESCRIPTION Imports?

4 msgs Oct 5

McDavid, Andrew Why can't NAMESPACE be a strict subset of DESCRIPTION Imports? Oct 4, 2016

Martin Morgan Why can't NAMESPACE be a strict subset of DESCRIPTION Imports? Oct 4, 2016

Dan Tenenbaum Why can't NAMESPACE be a strict subset of DESCRIPTION Imports? Oct 4, 2016

Martin Morgan Why can't NAMESPACE be a strict subset of DESCRIPTION Imports? Oct 5, 2016

[Bioc-devel] Harman not building on Windows due to mzR

4 msgs Oct 5

Jason.Ross at csiro.au Harman not building on Windows due to mzR Oct 4, 2016

Neumann, Steffen Harman not building on Windows due to mzR Oct 4, 2016

Jason.Ross at csiro.au Harman not building on Windows due to mzR Oct 5, 2016

Neumann, Steffen Harman not building on Windows due to mzR Oct 5, 2016

[Bioc-devel] package submission from bitbucket

3 msgs Oct 4

Lauren McIver package submission from bitbucket Oct 4, 2016

Shepherd, Lori package submission from bitbucket Oct 4, 2016

Lauren McIver package submission from bitbucket Oct 4, 2016

[Bioc-devel] Statistical Scalability for Streaming Data - 1/2 day workshop in London

1 msg Oct 4

Wolfgang Huber Statistical Scalability for Streaming Data - 1/2 day workshop in London Oct 4, 2016

[Bioc-devel] PKG_LIBS in make child processes

1 msg Oct 4

Ulrich Bodenhofer PKG_LIBS in make child processes Oct 4, 2016

[Bioc-devel] tokay1 (windows) build server cannot use the nbconvertR vignette engine

1 msg Oct 4

Angerer, Philipp tokay1 (windows) build server cannot use the nbconvertR vignette engine Oct 4, 2016

[Bioc-devel] "Feature-freeze" deadline for new packages

1 msg Oct 3

Marcel Ramos "Feature-freeze" deadline for new packages Oct 3, 2016

[Bioc-devel] OrgDbs for Bioconductor 3.4

1 msg Oct 3

Obenchain, Valerie OrgDbs for Bioconductor 3.4 Oct 3, 2016

[Bioc-devel] package review help

2 msgs Oct 1

Robert M. Flight package review help Sep 30, 2016

Martin Morgan package review help Oct 1, 2016

[Bioc-devel] package review help

1 msg Oct 1

Martin Morgan package review help Oct 1, 2016

Bioc-devel October 2016