Bioc-devel - November 2018 - Thread View

[Bioc-devel] Questions about some checks in the latest BiocCheck

4 msgs Nov 29

Casper Peters Questions about some checks in the latest BiocCheck Nov 28, 2018

Vincent Carey Questions about some checks in the latest BiocCheck Nov 28, 2018

Kasper Daniel Hansen Questions about some checks in the latest BiocCheck Nov 29, 2018

Michael Lawrence Questions about some checks in the latest BiocCheck Nov 29, 2018

[Bioc-devel] NEWS file, latest R/Bioc devel version

2 msgs Nov 28

Casper Peters NEWS file, latest R/Bioc devel version Nov 28, 2018

Shepherd, Lori NEWS file, latest R/Bioc devel version Nov 28, 2018

[Bioc-devel] Unable to install GenVisR from bioc release

3 msgs Nov 26

Skidmore, Zach Unable to install GenVisR from bioc release Nov 9, 2018

Obenchain, Valerie Unable to install GenVisR from bioc release Nov 9, 2018

Obenchain, Valerie Unable to install GenVisR from bioc release Nov 26, 2018

[Bioc-devel] merge the release and the dev version to eliminate errors

2 msgs Nov 25

Irene Zeng merge the release and the dev version to eliminate errors Nov 23, 2018

Obenchain, Valerie merge the release and the dev version to eliminate errors Nov 25, 2018

[Bioc-devel] Bioc 3.9 software builds Nov 23

1 msg Nov 23

Obenchain, Valerie Bioc 3.9 software builds Nov 23 Nov 23, 2018

[Bioc-devel] build/check report for experimental data not updating

2 msgs Nov 23

Carmen M. Livi build/check report for experimental data not updating Nov 23, 2018

Obenchain, Valerie build/check report for experimental data not updating Nov 23, 2018

[Bioc-devel] Cannot access remote upstream after changing the laptop

5 msgs Nov 21

Tang, Wenhao Cannot access remote upstream after changing the laptop Nov 21, 2018

Shepherd, Lori Cannot access remote upstream after changing the laptop Nov 21, 2018

Turaga, Nitesh Cannot access remote upstream after changing the laptop Nov 21, 2018

Tang, Wenhao 答复: Cannot access remote upstream after changing the laptop Nov 21, 2018

Dario Strbenac Cannot access remote upstream after changing the laptop Nov 21, 2018

[Bioc-devel] 80% of man pages must have runnable examples (package with numerous Shiny apps)

5 msgs Nov 21

L Rutter 80% of man pages must have runnable examples (package with numerous Shiny apps) Nov 19, 2018

Shepherd, Lori 80% of man pages must have runnable examples (package with numerous Shiny apps) Nov 19, 2018

Kevin RUE 80% of man pages must have runnable examples (package with numerous Shiny apps) Nov 19, 2018

L Rutter 80% of man pages must have runnable examples (package with numerous Shiny apps) Nov 21, 2018

Kevin RUE 80% of man pages must have runnable examples (package with numerous Shiny apps) Nov 21, 2018

[Bioc-devel] R 3.6 Compiling issues, are there any binaries available?

1 msg Nov 21

Casper Peters R 3.6 Compiling issues, are there any binaries available? Nov 21, 2018

[Bioc-devel] bioconductor git credentials

5 msgs Nov 20

Henning Redestig bioconductor git credentials Nov 20, 2018

Turaga, Nitesh bioconductor git credentials Nov 20, 2018

Henning Redestig bioconductor git credentials Nov 20, 2018

Turaga, Nitesh bioconductor git credentials Nov 20, 2018

Henning Redestig bioconductor git credentials Nov 20, 2018

[Bioc-devel] Duplicate issue in ELMER get.pair for HNSC data

1 msg Nov 20

ghafarpour Duplicate issue in ELMER get.pair for HNSC data Nov 20, 2018

[Bioc-devel] Manually editing man/.Rd files to pass BiocCheck

3 msgs Nov 18

L Rutter Manually editing man/.Rd files to pass BiocCheck Nov 18, 2018

Michael Lawrence Manually editing man/.Rd files to pass BiocCheck Nov 18, 2018

L Rutter Manually editing man/.Rd files to pass BiocCheck Nov 18, 2018

[Bioc-devel] use bioc docker images to reproduce linux build error?

4 msgs Nov 18

Paul Shannon use bioc docker images to reproduce linux build error? Nov 15, 2018

Obenchain, Valerie use bioc docker images to reproduce linux build error? Nov 16, 2018

Obenchain, Valerie use bioc docker images to reproduce linux build error? Nov 17, 2018

Paul Shannon use bioc docker images to reproduce linux build error? Nov 18, 2018

[Bioc-devel] failing Bioconductor package mlm4omics

1 msg Nov 17

Irene Zeng failing Bioconductor package mlm4omics Nov 17, 2018

[Bioc-devel] GenomicFeatures export request

1 msg Nov 15

Leonardo Collado Torres GenomicFeatures export request Nov 15, 2018

[Bioc-devel] Access to Bioconductor Git Credentials account

3 msgs Nov 14

Norman Pavelka Access to Bioconductor Git Credentials account Nov 14, 2018

Turaga, Nitesh Access to Bioconductor Git Credentials account Nov 14, 2018

Norman Pavelka Access to Bioconductor Git Credentials account Nov 14, 2018

[Bioc-devel] Possible to export coerce2() from S4Vectors?

8 msgs Nov 14

Bemis, Kylie Possible to export coerce2() from S4Vectors? Nov 13, 2018

Hervé Pagès Possible to export coerce2() from S4Vectors? Nov 13, 2018

Bemis, Kylie Possible to export coerce2() from S4Vectors? Nov 14, 2018

Michael Lawrence Possible to export coerce2() from S4Vectors? Nov 14, 2018

Bemis, Kylie Possible to export coerce2() from S4Vectors? Nov 14, 2018

Michael Lawrence Possible to export coerce2() from S4Vectors? Nov 14, 2018

Bemis, Kylie Possible to export coerce2() from S4Vectors? Nov 14, 2018

Michael Lawrence Possible to export coerce2() from S4Vectors? Nov 14, 2018

[Bioc-devel] Fwd: [bioc] DEXSeqHTML getListElement GRanges error

1 msg Nov 14

Lance Parsons DEXSeqHTML getListElement GRanges error Nov 14, 2018

[Bioc-devel] Single Package Builder for new package submission service Interruption

1 msg Nov 14

Shepherd, Lori Single Package Builder for new package submission service Interruption Nov 14, 2018

[Bioc-devel] submitting a tiny data package (GmapGenome.Hsapiens.rCRS)

5 msgs Nov 14

Tim Triche, Jr. submitting a tiny data package (GmapGenome.Hsapiens.rCRS) Nov 8, 2018

Obenchain, Valerie submitting a tiny data package (GmapGenome.Hsapiens.rCRS) Nov 9, 2018

Hervé Pagès submitting a tiny data package (GmapGenome.Hsapiens.rCRS) Nov 9, 2018

Shepherd, Lori submitting a tiny data package (GmapGenome.Hsapiens.rCRS) Nov 14, 2018

[Bioc-devel] Several vignettes with links between them

3 msgs Nov 14

David Jimenez-Morales Several vignettes with links between them Nov 13, 2018

Kevin RUE Several vignettes with links between them Nov 14, 2018

David Jimenez-Morales Several vignettes with links between them Nov 14, 2018

[Bioc-devel] Error : object 'lengths' is not exported by 'namespace:BiocGenerics'

6 msgs Nov 14

Hervé Pagès Error : object 'lengths' is not exported by 'namespace:BiocGenerics' Nov 2, 2018

Håkon Tjeldnes Error : object 'lengths' is not exported by 'namespace:BiocGenerics' Nov 2, 2018

Michael Lawrence Error : object 'lengths' is not exported by 'namespace:BiocGenerics' Nov 2, 2018

Håkon Tjeldnes Error : object 'lengths' is not exported by 'namespace:BiocGenerics' Nov 13, 2018

Hervé Pagès Error : object 'lengths' is not exported by 'namespace:BiocGenerics' Nov 13, 2018

Kasper Daniel Hansen Error : object 'lengths' is not exported by 'namespace:BiocGenerics' Nov 14, 2018

[Bioc-devel] A little confuse about how to update accepted package

10 msgs Nov 13

Tang, Wenhao A little confuse about how to update accepted package Nov 9, 2018

Martin Morgan A little confuse about how to update accepted package Nov 10, 2018

Kasper Daniel Hansen A little confuse about how to update accepted package Nov 10, 2018

Tang, Wenhao 答复: A little confuse about how to update accepted package Nov 11, 2018

Matthias Doering 答复: A little confuse about how to update accepted package Nov 11, 2018

Martin Morgan 答复: A little confuse about how to update accepted package Nov 11, 2018

Tang, Wenhao 答复: 答复: A little confuse about how to update accepted package Nov 13, 2018

Shepherd, Lori 答复: 答复: A little confuse about how to update accepted package Nov 13, 2018

Martin Morgan 答复: 答复: A little confuse about how to update accepted package Nov 13, 2018

Tang, Wenhao 答复: 答复: 答复: A little confuse about how to update accepted package Nov 13, 2018

[Bioc-devel] RFC: Bioc repository for single-version packages

2 msgs Nov 13

Martin Morgan RFC: Bioc repository for single-version packages Nov 5, 2018

Wolfgang Huber RFC: Bioc repository for single-version packages Nov 13, 2018

[Bioc-devel] What can I do if a depended package is not installed in Bioconductor build server

3 msgs Nov 8

Anh N Tran What can I do if a depended package is not installed in Bioconductor build server Nov 8, 2018

Obenchain, Valerie What can I do if a depended package is not installed in Bioconductor build server Nov 8, 2018

Anh N Tran What can I do if a depended package is not installed in Bioconductor build server Nov 8, 2018

[Bioc-devel] BiocManager and local Bioconductor mirror

3 msgs Nov 8

Rainer Johannes BiocManager and local Bioconductor mirror Nov 8, 2018

Martin Morgan BiocManager and local Bioconductor mirror Nov 8, 2018

[Bioc-devel] TIMEOUT in release and devel version of the package

1 msg Nov 7

Kangeyan, Divy TIMEOUT in release and devel version of the package Nov 7, 2018

[Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?

1 msg Nov 6

Leonardo Collado Torres How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE? Nov 6, 2018

[Bioc-devel] a pattern to be avoided? mcols(x)$y <- z

1 msg Nov 6

Hervé Pagès a pattern to be avoided? mcols(x)$y <- z Nov 6, 2018

[Bioc-devel] About the reproducibility of BioC server environment

3 msgs Nov 6

露崎弘毅 About the reproducibility of BioC server environment Nov 6, 2018

Martin Morgan About the reproducibility of BioC server environment Nov 6, 2018

Kasper Daniel Hansen About the reproducibility of BioC server environment Nov 6, 2018

[Bioc-devel] WARNING on tokay1 for SIAMCAT package

2 msgs Nov 6

Konrad Zych WARNING on tokay1 for SIAMCAT package Nov 6, 2018

Shepherd, Lori WARNING on tokay1 for SIAMCAT package Nov 6, 2018

[Bioc-devel] Commits not appearing in bioconductor build

4 msgs Nov 6

Clare Pacini Commits not appearing in bioconductor build Nov 6, 2018

Turaga, Nitesh Commits not appearing in bioconductor build Nov 6, 2018

Shepherd, Lori Commits not appearing in bioconductor build Nov 6, 2018

[Bioc-devel] Fwd: singscore problems reported in the Multiple platform build/check report for BioC 3.8

4 msgs Nov 5

Ruqian Lyu singscore problems reported in the Multiple platform build/check report for BioC 3.8 Nov 5, 2018

Mike Smith singscore problems reported in the Multiple platform build/check report for BioC 3.8 Nov 5, 2018

Martin Morgan singscore problems reported in the Multiple platform build/check report for BioC 3.8 Nov 5, 2018

Ruqian Lyu singscore problems reported in the Multiple platform build/check report for BioC 3.8 Nov 5, 2018

[Bioc-devel] How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE?

3 msgs Nov 5

Leonardo Collado Torres How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE? Nov 5, 2018

Martin Morgan How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE? Nov 5, 2018

Michael Lawrence How would you identify a package causing a NAMESPACE issue that you don't depend on in your DESCRIPTION/NAMESPACE? Nov 5, 2018

[Bioc-devel] Request upstream pull --force of sanitized master branch

1 msg Nov 5

Leonardo Collado Torres Request upstream pull --force of sanitized master branch Nov 5, 2018

[Bioc-devel] Request upstream pull --force of sanitized master branch

4 msgs Nov 5

Samuela Pollack Request upstream pull --force of sanitized master branch Nov 2, 2018

Turaga, Nitesh Request upstream pull --force of sanitized master branch Nov 5, 2018

Samuela Pollack Request upstream pull --force of sanitized master branch Nov 5, 2018

Turaga, Nitesh Request upstream pull --force of sanitized master branch Nov 5, 2018

[Bioc-devel] Initial list of deprecated packages for 3.9

1 msg Nov 5

Shepherd, Lori Initial list of deprecated packages for 3.9 Nov 5, 2018

[Bioc-devel] No curatedMetagenomicData build triggered

4 msgs Nov 5

Levi Waldron No curatedMetagenomicData build triggered Nov 3, 2018

Obenchain, Valerie No curatedMetagenomicData build triggered Nov 3, 2018

Levi Waldron No curatedMetagenomicData build triggered Nov 5, 2018

[Bioc-devel] macOS Mojave and R 3.6: issue with building some packages from source

1 msg Nov 4

Leonardo Collado Torres macOS Mojave and R 3.6: issue with building some packages from source Nov 4, 2018

[Bioc-devel] macOS Mojave and R 3.6: issue with building some packages from source

2 msgs Nov 4

Leonardo Collado Torres macOS Mojave and R 3.6: issue with building some packages from source Nov 2, 2018

Kasper Daniel Hansen macOS Mojave and R 3.6: issue with building some packages from source Nov 4, 2018

[Bioc-devel] choosing R version dependency for existing packages

4 msgs Nov 3

Paul Shannon choosing R version dependency for existing packages Nov 2, 2018

Martin Morgan choosing R version dependency for existing packages Nov 3, 2018

Paul Shannon choosing R version dependency for existing packages Nov 3, 2018

Henrik Bengtsson choosing R version dependency for existing packages Nov 3, 2018

[Bioc-devel] Bioconductor 3.9 builds and R 3.6

1 msg Nov 2

Obenchain, Valerie Bioconductor 3.9 builds and R 3.6 Nov 2, 2018

[Bioc-devel] Ask help to install gs tokay2 build/check

5 msgs Nov 2

Jianhong Ou, Ph.D. Ask help to install gs tokay2 build/check Nov 2, 2018

Kasper Daniel Hansen Ask help to install gs tokay2 build/check Nov 2, 2018

Jianhong Ou, Ph.D. Ask help to install gs tokay2 build/check Nov 2, 2018

Obenchain, Valerie Ask help to install gs tokay2 build/check Nov 2, 2018

Jianhong Ou, Ph.D. Ask help to install gs tokay2 build/check Nov 2, 2018

[Bioc-devel] GenomicFeatures

6 msgs Nov 2

Kasper Daniel Hansen GenomicFeatures Nov 2, 2018

Obenchain, Valerie GenomicFeatures Nov 2, 2018

Martin Morgan GenomicFeatures Nov 2, 2018

Kasper Daniel Hansen GenomicFeatures Nov 2, 2018

Obenchain, Valerie GenomicFeatures Nov 2, 2018

Hervé Pagès GenomicFeatures Nov 2, 2018

[Bioc-devel] query regarding bfg on bioconductor repository

2 msgs Nov 2

Turaga, Nitesh query regarding bfg on bioconductor repository Nov 2, 2018

[Bioc-devel] Warning in 'CHECK' report for Windows machine after release version bump

5 msgs Nov 1

Jakob Willforss Warning in 'CHECK' report for Windows machine after release version bump Nov 1, 2018

Christopher John Warning in 'CHECK' report for Windows machine after release version bump Nov 1, 2018

Obenchain, Valerie Warning in 'CHECK' report for Windows machine after release version bump Nov 1, 2018

Hervé Pagès Warning in 'CHECK' report for Windows machine after release version bump Nov 1, 2018

Obenchain, Valerie Warning in 'CHECK' report for Windows machine after release version bump Nov 1, 2018

Bioc-devel November 2018