Bioc-devel January 2018

"Duplicate commits" after when pushing change right after doing a clean `git clone git@git.bioconductor.org:packages/chimeraviz`

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6 msgs · Jan 13 – Jan 17

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Stian Lågstad "Duplicate commits" after when pushing change right after doing a clean `git clone git@git.bioconductor.org:packages/chimeraviz` Jan 13, 2018

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Turaga, Nitesh "Duplicate commits" after when pushing change right after doing a clean `git clone git@git.bioconductor.org:packages/chimeraviz` Jan 13, 2018

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Turaga, Nitesh "Duplicate commits" after when pushing change right after doing a clean `git clone git@git.bioconductor.org:packages/chimeraviz` Jan 17, 2018

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Stian Lågstad "Duplicate commits" after when pushing change right after doing a clean `git clone git@git.bioconductor.org:packages/chimeraviz` Jan 17, 2018

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Turaga, Nitesh "Duplicate commits" after when pushing change right after doing a clean `git clone git@git.bioconductor.org:packages/chimeraviz` Jan 17, 2018

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Laurent Gatto "Duplicate commits" after when pushing change right after doing a clean `git clone git@git.bioconductor.org:packages/chimeraviz` Jan 17, 2018

Alpha release of the iSEE visualization tool

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1 msg · Jan 31

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Aaron Lun Alpha release of the iSEE visualization tool Jan 31, 2018

BiocParallel and AnnotationDbi: database disk image is malformed

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8 msgs · Jan 19 – Jan 19

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Ludwig Geistlinger BiocParallel and AnnotationDbi: database disk image is malformed Jan 19, 2018

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Vincent Carey BiocParallel and AnnotationDbi: database disk image is malformed Jan 19, 2018

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Gabriel Becker BiocParallel and AnnotationDbi: database disk image is malformed Jan 19, 2018

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Martin Morgan BiocParallel and AnnotationDbi: database disk image is malformed Jan 19, 2018

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Martin Morgan BiocParallel and AnnotationDbi: database disk image is malformed Jan 19, 2018

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Ludwig Geistlinger BiocParallel and AnnotationDbi: database disk image is malformed Jan 19, 2018

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Martin Morgan BiocParallel and AnnotationDbi: database disk image is malformed Jan 19, 2018

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Ludwig Geistlinger BiocParallel and AnnotationDbi: database disk image is malformed Jan 19, 2018

BiocParallel: windows vs. mac/linux behavior

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2 msgs · Jan 31 – Jan 31

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Ludwig Geistlinger BiocParallel: windows vs. mac/linux behavior Jan 31, 2018

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Martin Morgan BiocParallel: windows vs. mac/linux behavior Jan 31, 2018

CINdex package build error in Linux

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O

Y

3 msgs · Jan 18 – Jan 19

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Krithika Bhuvaneshwar CINdex package build error in Linux Jan 18, 2018

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Obenchain, Valerie CINdex package build error in Linux Jan 19, 2018

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Yuriy Gusev CINdex package build error in Linux Jan 19, 2018

Can I push a new branch to Bioconductor git?

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2 msgs · Jan 7 – Jan 7

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Stian Lågstad Can I push a new branch to Bioconductor git? Jan 7, 2018

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Turaga, Nitesh Can I push a new branch to Bioconductor git? Jan 7, 2018

Changes to rhdf5

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A

3 msgs · Jan 5 – Jan 8

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Mike Smith Changes to rhdf5 Jan 5, 2018

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Aaron Lun Changes to rhdf5 Jan 5, 2018

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Mike Smith Changes to rhdf5 Jan 8, 2018

Changing package maintainer: git credentials

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2 msgs · Jan 13 – Jan 13

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Liz Ing-Simmons Changing package maintainer: git credentials Jan 13, 2018

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Turaga, Nitesh Changing package maintainer: git credentials Jan 13, 2018

Duplicate Commits in ASSIGN Package

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5 msgs · Jan 24 – Jan 31

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Jenkins, David Duplicate Commits in ASSIGN Package Jan 24, 2018

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Turaga, Nitesh Duplicate Commits in ASSIGN Package Jan 24, 2018

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Turaga, Nitesh Duplicate Commits in ASSIGN Package Jan 31, 2018

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Jenkins, David Duplicate Commits in ASSIGN Package Jan 31, 2018

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Turaga, Nitesh Duplicate Commits in ASSIGN Package Jan 31, 2018

Duplicate commit error when pushing to annotatr upstream/master

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3 msgs · Jan 8 – Jan 17

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Raymond Cavalcante Duplicate commit error when pushing to annotatr upstream/master Jan 8, 2018

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Turaga, Nitesh Duplicate commit error when pushing to annotatr upstream/master Jan 9, 2018

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Turaga, Nitesh Duplicate commit error when pushing to annotatr upstream/master Jan 17, 2018

Duplicate commits for hpar was [Re: Duplicate commits in Bioconductor commit history]

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3 msgs · Jan 19 – Jan 19

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Turaga, Nitesh Duplicate commits for hpar was [Re: Duplicate commits in Bioconductor commit history] Jan 19, 2018

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Turaga, Nitesh Duplicate commits for hpar was [Re: Duplicate commits in Bioconductor commit history] Jan 19, 2018

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Turaga, Nitesh Duplicate commits for hpar was [Re: Duplicate commits in Bioconductor commit history] Jan 19, 2018

Duplicate commits in Bioconductor commit history

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3 msgs · Jan 16 – Jan 17

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Laurent Gatto Duplicate commits in Bioconductor commit history Jan 16, 2018

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Laurent Gatto Duplicate commits in Bioconductor commit history Jan 17, 2018

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Turaga, Nitesh Duplicate commits in Bioconductor commit history Jan 17, 2018

EXTERNAL: Re: DOI for packages

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2 msgs · Jan 5 – Jan 5

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Nathan Sheffield EXTERNAL: Re: DOI for packages Jan 5, 2018

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Sean Davis EXTERNAL: Re: DOI for packages Jan 5, 2018

I cannot reproduce the error my package raises in production

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2 msgs · Jan 15 – Jan 15

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Carles Hernández I cannot reproduce the error my package raises in production Jan 15, 2018

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Martin Morgan I cannot reproduce the error my package raises in production Jan 15, 2018

Issue with dependencies on Windows (tokay2)

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2 msgs · Jan 3 – Jan 4

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Hoffman, Gabriel Issue with dependencies on Windows (tokay2) Jan 3, 2018

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Obenchain, Valerie Issue with dependencies on Windows (tokay2) Jan 4, 2018

Linking up to polyester and ballgown

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2 msgs · Jan 29 – Jan 29

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Jack Fu Linking up to polyester and ballgown Jan 29, 2018

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Obenchain, Valerie Linking up to polyester and ballgown Jan 29, 2018

List of Deprecated Packages for Bioc3.7

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1 msg · Jan 19

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Shepherd, Lori List of Deprecated Packages for Bioc3.7 Jan 19, 2018

Missing link files in Windows (release and devel)

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7 msgs · Jan 16 – Jan 17

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Leonardo Collado Torres Missing link files in Windows (release and devel) Jan 16, 2018

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Martin Morgan Missing link files in Windows (release and devel) Jan 16, 2018

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Leonardo Collado Torres Missing link files in Windows (release and devel) Jan 17, 2018

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James W. MacDonald Missing link files in Windows (release and devel) Jan 17, 2018

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Stephanie M. Gogarten Missing link files in Windows (release and devel) Jan 17, 2018

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Leonardo Collado Torres Missing link files in Windows (release and devel) Jan 17, 2018

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Martin Morgan Missing link files in Windows (release and devel) Jan 17, 2018

NanoStringDiff package update

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11 msgs · Jan 24 – Jan 26

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Zhai, Tingting NanoStringDiff package update Jan 24, 2018

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Shepherd, Lori NanoStringDiff package update Jan 25, 2018

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Shepherd, Lori NanoStringDiff package update Jan 25, 2018

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Zhai, Tingting NanoStringDiff package update Jan 25, 2018

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Shepherd, Lori NanoStringDiff package update Jan 25, 2018

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Zhai, Tingting NanoStringDiff package update Jan 25, 2018

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Shepherd, Lori NanoStringDiff package update Jan 25, 2018

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Zhai, Tingting NanoStringDiff package update Jan 25, 2018

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Shepherd, Lori NanoStringDiff package update Jan 25, 2018

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Zhai, Tingting NanoStringDiff package update Jan 25, 2018

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Shepherd, Lori NanoStringDiff package update Jan 26, 2018

New NSF funding opportunity: Rules of Life (RoL): Forecasting and Emergence in Living Systems

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1 msg · Jan 2

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Sean Davis New NSF funding opportunity: Rules of Life (RoL): Forecasting and Emergence in Living Systems Jan 2, 2018

No write permissions to push changes to my devel package

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2 msgs · Jan 11 – Jan 11

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Andreas Kapouranis No write permissions to push changes to my devel package Jan 11, 2018

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Turaga, Nitesh No write permissions to push changes to my devel package Jan 11, 2018

Numeric Operation on DataFrame

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3 msgs · Jan 15 – Jan 16

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Dario Strbenac Numeric Operation on DataFrame Jan 15, 2018

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Michael Lawrence Numeric Operation on DataFrame Jan 16, 2018

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Hervé Pagès Numeric Operation on DataFrame Jan 16, 2018

Permission denied when fetching from BioC GitHub repository

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6 msgs · Jan 23 – Jan 24

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Federico C Permission denied when fetching from BioC GitHub repository Jan 23, 2018

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Obenchain, Valerie Permission denied when fetching from BioC GitHub repository Jan 23, 2018

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Federico C Permission denied when fetching from BioC GitHub repository Jan 23, 2018

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Federico C Permission denied when fetching from BioC GitHub repository Jan 24, 2018

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Turaga, Nitesh Permission denied when fetching from BioC GitHub repository Jan 24, 2018

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Federico C Permission denied when fetching from BioC GitHub repository Jan 24, 2018

Problems creating a new GitHub repository for an existing Bioconductor package

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2 msgs · Jan 16 – Jan 16

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Pau Bellot Pujalte Problems creating a new GitHub repository for an existing Bioconductor package Jan 16, 2018

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Turaga, Nitesh Problems creating a new GitHub repository for an existing Bioconductor package Jan 16, 2018

Push to git not updating correctly

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2 msgs · Jan 19 – Jan 22

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Clare Pacini Push to git not updating correctly Jan 19, 2018

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Turaga, Nitesh Push to git not updating correctly Jan 22, 2018

Question regarding potential package

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2 msgs · Jan 16 – Jan 16

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Rupji, Manali Question regarding potential package Jan 16, 2018

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Martin Morgan Question regarding potential package Jan 16, 2018

RSS feed on bioconductor.org/developers/gitlog

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5 msgs · Jan 2 – Jan 5

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Turaga, Nitesh RSS feed on bioconductor.org/developers/gitlog Jan 2, 2018

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Obenchain, Valerie RSS feed on bioconductor.org/developers/gitlog Jan 2, 2018

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Lluís Revilla RSS feed on bioconductor.org/developers/gitlog Jan 3, 2018

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Turaga, Nitesh RSS feed on bioconductor.org/developers/gitlog Jan 3, 2018

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Turaga, Nitesh RSS feed on bioconductor.org/developers/gitlog Jan 5, 2018

Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

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8 msgs · Jan 24 – Jan 30

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Wolfgang Huber Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ? Jan 24, 2018

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Martin Morgan Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ? Jan 26, 2018

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Vincent Carey Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ? Jan 26, 2018

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Tim Triche, Jr. Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ? Jan 26, 2018

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Hervé Pagès Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ? Jan 26, 2018

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Wolfgang Huber Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ? Jan 26, 2018

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Kasper Daniel Hansen Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ? Jan 26, 2018

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Hervé Pagès Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ? Jan 30, 2018

Updated Deprecated Package List for Bioc 3.7

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1 msg · Jan 5

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Shepherd, Lori Updated Deprecated Package List for Bioc 3.7 Jan 5, 2018

Version bumps

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Y

4 msgs · Jan 19 – Jan 25

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Martin Morgan Version bumps Jan 19, 2018

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Yuande Tan Version bumps Jan 22, 2018

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Martin Morgan Version bumps Jan 23, 2018

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Martin Morgan Version bumps Jan 25, 2018

Vignettes location in BiocCheck vs R CMD check

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6 msgs · Jan 29 – Jan 29

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Armen Abnousi Vignettes location in BiocCheck vs R CMD check Jan 29, 2018

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Martin Morgan Vignettes location in BiocCheck vs R CMD check Jan 29, 2018

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Diego Morais Vignettes location in BiocCheck vs R CMD check Jan 29, 2018

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Armen Abnousi Vignettes location in BiocCheck vs R CMD check Jan 29, 2018

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Kasper Daniel Hansen Vignettes location in BiocCheck vs R CMD check Jan 29, 2018

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Armen Abnousi Vignettes location in BiocCheck vs R CMD check Jan 29, 2018

cannot fetch upstream git

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2 msgs · Jan 30 – Jan 31

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bruno contrino cannot fetch upstream git Jan 30, 2018

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Obenchain, Valerie cannot fetch upstream git Jan 31, 2018

chipenrich bioc builds timeout not reproducible

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O

2 msgs · Jan 8 – Jan 8

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Raymond Cavalcante chipenrich bioc builds timeout not reproducible Jan 8, 2018

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Obenchain, Valerie chipenrich bioc builds timeout not reproducible Jan 8, 2018

conditions on vectors of length > 1 Warning/ERROR

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1 msg · Jan 25

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Shepherd, Lori conditions on vectors of length > 1 Warning/ERROR Jan 25, 2018

conditions on vectors of length > 1 Warning/ERROR

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2 msgs · Jan 27 – Jan 29

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Charles Warden conditions on vectors of length > 1 Warning/ERROR Jan 27, 2018

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Shepherd, Lori conditions on vectors of length > 1 Warning/ERROR Jan 29, 2018

differential expression tools for proteins

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3 msgs · Jan 6 – Jan 7

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Cardin Julie differential expression tools for proteins Jan 6, 2018

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Diego Morais differential expression tools for proteins Jan 6, 2018

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Wolfgang Huber differential expression tools for proteins Jan 7, 2018

ensembl release build policy update and potential need to update Bioconductor code

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1 msg · Jan 8

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Shepherd, Lori ensembl release build policy update and potential need to update Bioconductor code Jan 8, 2018

error in loading pbdMPI on tokay2

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2 msgs · Jan 27 – Jan 31

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Armen Abnousi error in loading pbdMPI on tokay2 Jan 27, 2018

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Obenchain, Valerie error in loading pbdMPI on tokay2 Jan 31, 2018

git help

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12 msgs · Jan 3 – Jan 9

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Kevin Horan git help Jan 3, 2018

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Turaga, Nitesh git help Jan 3, 2018

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Kevin Horan git help Jan 3, 2018

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Turaga, Nitesh git help Jan 4, 2018

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Turaga, Nitesh git help Jan 5, 2018

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Kevin Horan git help Jan 7, 2018

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Turaga, Nitesh git help Jan 7, 2018

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Turaga, Nitesh git help Jan 7, 2018

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Turaga, Nitesh git help Jan 7, 2018

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Kevin Horan git help Jan 8, 2018

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Turaga, Nitesh git help Jan 9, 2018

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Kevin Horan git help Jan 9, 2018

git permission denied to synapter repository

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3 msgs · Jan 17 – Jan 17

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Sebastian Gibb git permission denied to synapter repository Jan 17, 2018

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Turaga, Nitesh git permission denied to synapter repository Jan 17, 2018

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Sebastian Gibb git permission denied to synapter repository Jan 17, 2018

mzR build failure on Windows: missing HDF5 libraries

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7 msgs · Jan 2 – Jan 11

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Neumann, Steffen mzR build failure on Windows: missing HDF5 libraries Jan 2, 2018

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Martin Morgan mzR build failure on Windows: missing HDF5 libraries Jan 2, 2018

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Mike Smith mzR build failure on Windows: missing HDF5 libraries Jan 3, 2018

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Martin Morgan mzR build failure on Windows: missing HDF5 libraries Jan 5, 2018

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Neumann, Steffen mzR build failure on Windows: missing HDF5 libraries Jan 7, 2018

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Rainer Johannes mzR build failure on Windows: missing HDF5 libraries Jan 7, 2018

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Neumann, Steffen mzR build failure on Windows: missing HDF5 libraries Jan 11, 2018

need git push permission for mtbls2

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2 msgs · Jan 19 – Jan 19

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Neumann, Steffen need git push permission for mtbls2 Jan 19, 2018

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Turaga, Nitesh need git push permission for mtbls2 Jan 19, 2018

not all bioc packages visible on github?

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R

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3 msgs · Jan 24 – Jan 25

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Paul Shannon not all bioc packages visible on github? Jan 24, 2018

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Robert M. Flight not all bioc packages visible on github? Jan 24, 2018

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Mike Smith not all bioc packages visible on github? Jan 25, 2018

project templating tools

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N

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3 msgs · Jan 21 – Jan 22

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Vincent Carey project templating tools Jan 21, 2018

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Nima Hejazi project templating tools Jan 21, 2018

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Michael Lawrence project templating tools Jan 22, 2018

search - was: differential expression tools for proteins

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2 msgs · Jan 7 – Jan 8

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Wolfgang Huber search - was: differential expression tools for proteins Jan 7, 2018

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Martin Morgan search - was: differential expression tools for proteins Jan 8, 2018

segfaults in findOverlaps()

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1 msg · Jan 8

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Hervé Pagès segfaults in findOverlaps() Jan 8, 2018

unable to push to bioconductor git

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2 msgs · Jan 18 – Jan 18

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Davy Cats unable to push to bioconductor git Jan 18, 2018

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Turaga, Nitesh unable to push to bioconductor git Jan 18, 2018

updating Bioconductor package that is already on Github

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10 msgs · Jan 26 – Jan 31

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Simina Boca updating Bioconductor package that is already on Github Jan 26, 2018

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Turaga, Nitesh updating Bioconductor package that is already on Github Jan 26, 2018

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Simina Boca updating Bioconductor package that is already on Github Jan 26, 2018

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Turaga, Nitesh updating Bioconductor package that is already on Github Jan 26, 2018

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Simina Boca updating Bioconductor package that is already on Github Jan 28, 2018

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Simina Boca updating Bioconductor package that is already on Github Jan 30, 2018

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Turaga, Nitesh updating Bioconductor package that is already on Github Jan 30, 2018

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Simina Boca updating Bioconductor package that is already on Github Jan 30, 2018

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Turaga, Nitesh updating Bioconductor package that is already on Github Jan 31, 2018

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Simina Boca updating Bioconductor package that is already on Github Jan 31, 2018