Bioc-devel - March 2020 - Thread View

[Bioc-devel] Final List of Deprecated Packages for Bioc3.11

2 msgs Mar 31

Shepherd, Lori Final List of Deprecated Packages for Bioc3.11 Mar 30, 2020

Shepherd, Lori Final List of Deprecated Packages for Bioc3.11 Mar 31, 2020

[Bioc-devel] How can I maintain a stable list of source urls

1 msg Mar 31

Tim Sears How can I maintain a stable list of source urls Mar 31, 2020

[Bioc-devel] Bioc2020 - Call for BOF/HAK/FAQ Sections

1 msg Mar 31

Shepherd, Lori Bioc2020 - Call for BOF/HAK/FAQ Sections Mar 31, 2020

[Bioc-devel] The errror from build report of ASpediaFI

2 msgs Mar 31

Bioinformatics NCC The errror from build report of ASpediaFI Mar 30, 2020

Shepherd, Lori The errror from build report of ASpediaFI Mar 31, 2020

[Bioc-devel] Deadline for devel branch 3.11 to pass R CMD build and R CMD check

1 msg Mar 30

Shepherd, Lori Deadline for devel branch 3.11 to pass R CMD build and R CMD check Mar 30, 2020

[Bioc-devel] Bioconductor Release 3.10 Code Freeze Deadline

1 msg Mar 30

Shepherd, Lori Bioconductor Release 3.10 Code Freeze Deadline Mar 30, 2020

[Bioc-devel] New Package and New Docker Image Submission Deadline for Bioc Release 3.11

2 msgs Mar 30

Shepherd, Lori New Package and New Docker Image Submission Deadline for Bioc Release 3.11 Mar 13, 2020

Shepherd, Lori New Package and New Docker Image Submission Deadline for Bioc Release 3.11 Mar 30, 2020

[Bioc-devel] Docker image submission

3 msgs Mar 30

Carlos Biagi Jr Docker image submission Mar 29, 2020

Martin Morgan Docker image submission Mar 30, 2020

Carlos Biagi Jr Docker image submission Mar 30, 2020

[Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

8 msgs Mar 30

Turaga, Nitesh Trying to access the source repository of a bioconductor package (Developer Access) Mar 27, 2020

Enio Gjerga Trying to access the source repository of a bioconductor package (Developer Access) Mar 30, 2020

Shepherd, Lori Trying to access the source repository of a bioconductor package (Developer Access) Mar 30, 2020

Enio Gjerga Trying to access the source repository of a bioconductor package (Developer Access) Mar 30, 2020

Shepherd, Lori Trying to access the source repository of a bioconductor package (Developer Access) Mar 30, 2020

Turaga, Nitesh Trying to access the source repository of a bioconductor package (Developer Access) Mar 30, 2020

Enio Gjerga Trying to access the source repository of a bioconductor package (Developer Access) Mar 30, 2020

Shepherd, Lori Trying to access the source repository of a bioconductor package (Developer Access) Mar 30, 2020

[Bioc-devel] 'MACSQuantifyR' Bioconductor package

2 msgs Mar 30

Raphael Bonnet 'MACSQuantifyR' Bioconductor package Mar 30, 2020

Turaga, Nitesh 'MACSQuantifyR' Bioconductor package Mar 30, 2020

[Bioc-devel] Problems caused by earlier Rhtslib migration

1 msg Mar 30

Antti Honkela Problems caused by earlier Rhtslib migration Mar 30, 2020

[Bioc-devel] BiocCredentials email issue

2 msgs Mar 29

Matt Wilkerson BiocCredentials email issue Mar 28, 2020

Turaga, Nitesh BiocCredentials email issue Mar 29, 2020

[Bioc-devel] Re phospphonormalizer package

1 msg Mar 29

Turaga, Nitesh Re phospphonormalizer package Mar 29, 2020

[Bioc-devel] core dump in MotifDb build

6 msgs Mar 28

Paul Shannon core dump in MotifDb build Mar 26, 2020

Hervé Pagès core dump in MotifDb build Mar 26, 2020

Martin Morgan core dump in MotifDb build Mar 27, 2020

Paul Shannon core dump in MotifDb build Mar 27, 2020

Robert Castelo core dump in MotifDb build Mar 27, 2020

Martin Morgan core dump in MotifDb build Mar 28, 2020

[Bioc-devel] Re phospphonormalizer package

1 msg Mar 28

Sohrab Saraei Re phospphonormalizer package Mar 28, 2020

[Bioc-devel] Help with tokay2 errors

1 msg Mar 28

Benjamin Jean-Marie Tremblay Help with tokay2 errors Mar 28, 2020

[Bioc-devel] Fwd: Trying to access the source repository of a bioconductor package (Developer Access)

1 msg Mar 27

Turaga, Nitesh Trying to access the source repository of a bioconductor package (Developer Access) Mar 27, 2020

[Bioc-devel] Question regarding the error from build report

3 msgs Mar 27

유도영 Question regarding the error from build report Mar 26, 2020

Hervé Pagès Question regarding the error from build report Mar 26, 2020

Michael Lawrence Question regarding the error from build report Mar 27, 2020

[Bioc-devel] Trying to access the source repository of a bioconductor package (Developer Access)

6 msgs Mar 27

Enio Gjerga Trying to access the source repository of a bioconductor package (Developer Access) Mar 27, 2020

Turaga, Nitesh Trying to access the source repository of a bioconductor package (Developer Access) Mar 27, 2020

Enio Gjerga Trying to access the source repository of a bioconductor package (Developer Access) Mar 27, 2020

Turaga, Nitesh Trying to access the source repository of a bioconductor package (Developer Access) Mar 27, 2020

Enio Gjerga Trying to access the source repository of a bioconductor package (Developer Access) Mar 27, 2020

Turaga, Nitesh Trying to access the source repository of a bioconductor package (Developer Access) Mar 27, 2020

[Bioc-devel] Bioconductor 3.11 db0s are available

1 msg Mar 27

Interdonato, Kayla Bioconductor 3.11 db0s are available Mar 27, 2020

[Bioc-devel] Drosophila virilis BioPackage forthcoming?

2 msgs Mar 26

Ilkka Havukkala Drosophila virilis BioPackage forthcoming? Mar 26, 2020

Hervé Pagès Drosophila virilis BioPackage forthcoming? Mar 26, 2020

[Bioc-devel] Fwd: 'MBQN' Bioconductor package

2 msgs Mar 26

Eva Brombacher 'MBQN' Bioconductor package Mar 26, 2020

Shepherd, Lori 'MBQN' Bioconductor package Mar 26, 2020

[Bioc-devel] New package function question

2 msgs Mar 26

ELENI ADAM New package function question Mar 24, 2020

Martin Morgan New package function question Mar 26, 2020

[Bioc-devel] Bioconductor package IMMAN

4 msgs Mar 26

Minoo Ashtiani Bioconductor package IMMAN Mar 23, 2020

Shepherd, Lori Bioconductor package IMMAN Mar 23, 2020

Minoo Ashtiani Bioconductor package IMMAN Mar 26, 2020

Shepherd, Lori Bioconductor package IMMAN Mar 26, 2020

[Bioc-devel] Python dependency

4 msgs Mar 26

Daniele Muraro Python dependency Mar 24, 2020

Hervé Pagès Python dependency Mar 24, 2020

Martin Morgan Python dependency Mar 24, 2020

Daniele Muraro Python dependency [EXT] Mar 26, 2020

[Bioc-devel] news on tidybulk?

8 msgs Mar 26

stefano iacus news on tidybulk? Mar 24, 2020

Shepherd, Lori news on tidybulk? Mar 24, 2020

Vincent Carey news on tidybulk? Mar 24, 2020

stefano iacus news on tidybulk? Mar 24, 2020

stefano iacus news on tidybulk? Mar 26, 2020

[Bioc-devel] Problem updating Bioconductor package

2 msgs Mar 25

Hong Zheng Problem updating Bioconductor package Mar 24, 2020

Turaga, Nitesh Problem updating Bioconductor package Mar 25, 2020

[Bioc-devel] Trouble accessing packages

3 msgs Mar 24

Enio Gjerga Trouble accessing packages Mar 24, 2020

Shepherd, Lori Trouble accessing packages Mar 24, 2020

[Bioc-devel] Request for activating Bioconductor repository account for Lumi and methyAnalysis package

3 msgs Mar 24

Huang, Lei [CRI] Request for activating Bioconductor repository account for Lumi and methyAnalysis package Mar 23, 2020

Huang, Lei [CRI] Help needed on BioC Git credential for package maintainer Mar 24, 2020

Turaga, Nitesh Help needed on BioC Git credential for package maintainer Mar 24, 2020

[Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

16 msgs Mar 24

Charles Warden Issue Reproducing BioC 3.11 COHCAP Error Message Mar 17, 2020

Shepherd, Lori Issue Reproducing BioC 3.11 COHCAP Error Message Mar 19, 2020

Charles Warden Issue Reproducing BioC 3.11 COHCAP Error Message Mar 19, 2020

Shepherd, Lori Issue Reproducing BioC 3.11 COHCAP Error Message Mar 19, 2020

Charles Warden Issue Reproducing BioC 3.11 COHCAP Error Message Mar 19, 2020

Shepherd, Lori Issue Reproducing BioC 3.11 COHCAP Error Message Mar 19, 2020

Alexey Sergushichev Issue Reproducing BioC 3.11 COHCAP Error Message Mar 19, 2020

Charles Warden Issue Reproducing BioC 3.11 COHCAP Error Message Mar 19, 2020

Charles Warden Issue Reproducing BioC 3.11 COHCAP Error Message Mar 20, 2020

Martin Morgan Issue Reproducing BioC 3.11 COHCAP Error Message Mar 20, 2020

Charles Warden Issue Reproducing BioC 3.11 COHCAP Error Message Mar 20, 2020

Martin Morgan Issue Reproducing BioC 3.11 COHCAP Error Message Mar 20, 2020

Charles Warden Issue Reproducing BioC 3.11 COHCAP Error Message Mar 20, 2020

Charles Warden Issue Reproducing BioC 3.11 COHCAP Error Message Mar 23, 2020

Shepherd, Lori Issue Reproducing BioC 3.11 COHCAP Error Message Mar 24, 2020

Charles Warden Issue Reproducing BioC 3.11 COHCAP Error Message Mar 24, 2020

[Bioc-devel] issue 1333 tscR package accepted

3 msgs Mar 24

Fernando Pérez issue 1333 tscR package accepted Mar 24, 2020

Shepherd, Lori issue 1333 tscR package accepted Mar 24, 2020

[Bioc-devel] Problems with BiocCredentials

2 msgs Mar 23

Saskia Freytag Problems with BiocCredentials Mar 22, 2020

Turaga, Nitesh Problems with BiocCredentials Mar 23, 2020

[Bioc-devel] proper way to define an S4 method for 'plot'

6 msgs Mar 20

Vincent Carey proper way to define an S4 method for 'plot' Mar 16, 2020

Henrik Bengtsson proper way to define an S4 method for 'plot' Mar 16, 2020

Michael Lawrence proper way to define an S4 method for 'plot' Mar 16, 2020

Martin Morgan proper way to define an S4 method for 'plot' Mar 16, 2020

Shepherd, Lori proper way to define an S4 method for 'plot' Mar 19, 2020

Laurent Gatto proper way to define an S4 method for 'plot' Mar 20, 2020

[Bioc-devel] INSPEcT vignette building issue

1 msg Mar 20

Mattia Furlan INSPEcT vignette building issue Mar 20, 2020

[Bioc-devel] R CMD build error for 3.10 (but not 3.11)

14 msgs Mar 20

L Rutter R CMD build error for 3.10 (but not 3.11) Mar 3, 2020

Shepherd, Lori R CMD build error for 3.10 (but not 3.11) Mar 3, 2020

L Rutter R CMD build error for 3.10 (but not 3.11) Mar 10, 2020

Shepherd, Lori R CMD build error for 3.10 (but not 3.11) Mar 10, 2020

L Rutter R CMD build error for 3.10 (but not 3.11) Mar 11, 2020

Shepherd, Lori R CMD build error for 3.10 (but not 3.11) Mar 12, 2020

L Rutter R CMD build error for 3.10 (but not 3.11) Mar 15, 2020

Turaga, Nitesh R CMD build error for 3.10 (but not 3.11) Mar 15, 2020

Shepherd, Lori R CMD build error for 3.10 (but not 3.11) Mar 15, 2020

L Rutter R CMD build error for 3.10 (but not 3.11) Mar 15, 2020

Shepherd, Lori R CMD build error for 3.10 (but not 3.11) Mar 16, 2020

L Rutter R CMD build error for 3.10 (but not 3.11) Mar 20, 2020

Shepherd, Lori R CMD build error for 3.10 (but not 3.11) Mar 20, 2020

[Bioc-devel] help with Win10 TLS problem?

1 msg Mar 19

Hervé Pagès help with Win10 TLS problem? Mar 19, 2020

[Bioc-devel] BiSeq package

2 msgs Mar 19

Katja Hebestreit BiSeq package Mar 18, 2020

Shepherd, Lori BiSeq package Mar 19, 2020

[Bioc-devel] Bioconductor Developers Forum - Thursday 19th March

2 msgs Mar 19

Mike Smith Bioconductor Developers Forum - Thursday 19th March Mar 16, 2020

Mike Smith Bioconductor Developers Forum - Thursday 19th March Mar 19, 2020

[Bioc-devel] help with Win10 TSL problem?

4 msgs Mar 18

Egon Willighagen help with Win10 TSL problem? Mar 18, 2020

Neumann, Steffen help with Win10 TLS problem? Mar 18, 2020

Hervé Pagès help with Win10 TLS problem? Mar 18, 2020

[Bioc-devel] Change associated email/github

1 msg Mar 18

Turaga, Nitesh Change associated email/github Mar 18, 2020

[Bioc-devel] Change associated email/github

4 msgs Mar 18

Russell Bainer Change associated email/github Mar 17, 2020

Turaga, Nitesh Change associated email/github Mar 17, 2020

Russell Bainer Change associated email/github Mar 17, 2020

Turaga, Nitesh Change associated email/github Mar 18, 2020

[Bioc-devel] Deploy a critical patch

2 msgs Mar 18

Julian Flesch Deploy a critical patch Mar 17, 2020

Sean Davis Deploy a critical patch Mar 18, 2020

[Bioc-devel] Push the updated package to Bioconductor

2 msgs Mar 17

Ruijia Wang Push the updated package to Bioconductor Mar 17, 2020

Shepherd, Lori Push the updated package to Bioconductor Mar 17, 2020

[Bioc-devel] BiocParallel Variable Not Found

5 msgs Mar 17

Dario Strbenac BiocParallel Variable Not Found Mar 17, 2020

Martin Morgan BiocParallel Variable Not Found Mar 17, 2020

Dario Strbenac BiocParallel Variable Not Found Mar 17, 2020

Martin Morgan BiocParallel Variable Not Found Mar 17, 2020

Dario Strbenac BiocParallel Variable Not Found Mar 17, 2020

[Bioc-devel] regionReport error: leads to potential disk space issues for ImageMagick

1 msg Mar 17

Leonardo Collado Torres regionReport error: leads to potential disk space issues for ImageMagick Mar 17, 2020

[Bioc-devel] Fw: Bioconductor package SIM

3 msgs Mar 17

r@me@ezes m@iii@g oii @ki@@i Bioconductor package SIM Mar 17, 2020

Turaga, Nitesh Bioconductor package SIM Mar 17, 2020

[Bioc-devel] Cairo error in Windows server

2 msgs Mar 16

Yue Zhao (Jason) Cairo error in Windows server Mar 16, 2020

Shepherd, Lori Cairo error in Windows server Mar 16, 2020

[Bioc-devel] XINA additional maintainers

4 msgs Mar 12

Singh, Sasha A.,Ph.D. XINA additional maintainers Mar 10, 2020

Turaga, Nitesh XINA additional maintainers Mar 12, 2020

Singh, Sasha A.,Ph.D. XINA additional maintainers Mar 12, 2020

Turaga, Nitesh XINA additional maintainers Mar 12, 2020

[Bioc-devel] Update to devel builders

1 msg Mar 12

Shepherd, Lori Update to devel builders Mar 12, 2020

[Bioc-devel] commit access to the Bioconductor Git repository of multtest package

5 msgs Mar 11

Yongchao Ge commit access to the Bioconductor Git repository of multtest package Mar 11, 2020

Turaga, Nitesh commit access to the Bioconductor Git repository of multtest package Mar 11, 2020

Katie Pollard commit access to the Bioconductor Git repository of multtest package Mar 11, 2020

Turaga, Nitesh commit access to the Bioconductor Git repository of multtest package Mar 11, 2020

Yongchao Ge commit access to the Bioconductor Git repository of multtest package Mar 11, 2020

[Bioc-devel] Bioconductor Release 3.11 Schedule

2 msgs Mar 11

Shepherd, Lori Bioconductor Release 3.11 Schedule Mar 10, 2020

Turaga, Nitesh Bioconductor Release 3.11 Schedule Mar 11, 2020

[Bioc-devel] Fwd: Bioconductor package multtest

1 msg Mar 10

Katie Pollard Bioconductor package multtest Mar 10, 2020

[Bioc-devel] BioC2019 Code of Conduct violation response

1 msg Mar 9

Levi Waldron BioC2019 Code of Conduct violation response Mar 9, 2020

[Bioc-devel] Class for differentially expressed genes?

5 msgs Mar 9

Roman Hillje Class for differentially expressed genes? Mar 9, 2020

Shepherd, Lori Class for differentially expressed genes? Mar 9, 2020

Constantin Ahlmann-Eltze Class for differentially expressed genes? Mar 9, 2020

Vincent Carey Class for differentially expressed genes? Mar 9, 2020

Roman Hillje Class for differentially expressed genes? Mar 9, 2020

[Bioc-devel] Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased)

7 msgs Mar 9

Ulrich Bodenhofer Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased) Mar 7, 2020

Vincent Carey Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased) Mar 7, 2020

Shepherd, Lori Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased) Mar 7, 2020

Vincent Carey Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased) Mar 7, 2020

Felix Ernst Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased) Mar 7, 2020

Ulrich Bodenhofer Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased) Mar 9, 2020

Hervé Pagès Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased) Mar 9, 2020

[Bioc-devel] MRD measurements in Leukemic patients using NGS data in r

10 msgs Mar 8

Mulder, R MRD measurements in Leukemic patients using NGS data in r Mar 4, 2020

Tim Triche, Jr. MRD measurements in Leukemic patients using NGS data in r Mar 5, 2020

Tim Triche, Jr. MRD measurements in Leukemic patients using NGS data in r Mar 6, 2020

Mulder, R MRD measurements in Leukemic patients using NGS data in r Mar 7, 2020

Tim Triche, Jr. MRD measurements in Leukemic patients using NGS data in r Mar 7, 2020

Mulder, R MRD measurements in Leukemic patients using NGS data in r Mar 8, 2020

Vincent Carey MRD measurements in Leukemic patients using NGS data in r Mar 8, 2020

Mulder, R MRD measurements in Leukemic patients using NGS data in r Mar 8, 2020

Tim Triche, Jr. MRD measurements in Leukemic patients using NGS data in r Mar 8, 2020

[Bioc-devel] MRD measurements in Leukemic patients using NGS data in r

1 msg Mar 6

Tim Triche, Jr. MRD measurements in Leukemic patients using NGS data in r Mar 6, 2020

[Bioc-devel] [rOpenSci] Community Call: Maintaining an R Package

1 msg Mar 5

Leonardo Collado Torres Community Call: Maintaining an R Package Mar 5, 2020

[Bioc-devel] CDSB Workshop 2020: Building workflows with RStudio and Bioconductor for single cell RNA-seq analysis

2 msgs Mar 5

Leonardo Collado Torres CDSB Workshop 2020: Building workflows with RStudio and Bioconductor for single cell RNA-seq analysis Mar 5, 2020

[Bioc-devel] how to get write permission of my R Bioconductor package to Bioconductor github

3 msgs Mar 4

Turaga, Nitesh how to get write permission of my R Bioconductor package to Bioconductor github Mar 4, 2020

weiliang Qiu how to get write permission of my R Bioconductor package to Bioconductor github Mar 4, 2020

[Bioc-devel] Dependency files question

2 msgs Mar 4

Alexandru Voda Dependency files question Mar 2, 2020

Shepherd, Lori Dependency files question Mar 4, 2020

[Bioc-devel] Change citation reference

1 msg Mar 3

Shepherd, Lori Change citation reference Mar 3, 2020

[Bioc-devel] Reverting on the 'master' branch

8 msgs Mar 3

Roel Janssen Reverting on the 'master' branch Mar 2, 2020

Turaga, Nitesh Reverting on the 'master' branch Mar 2, 2020

Roel Janssen Reverting on the 'master' branch Mar 2, 2020

Turaga, Nitesh Reverting on the 'master' branch Mar 2, 2020

Roel Janssen Reverting on the 'master' branch Mar 2, 2020

Turaga, Nitesh Reverting on the 'master' branch Mar 3, 2020

Martin Morgan Reverting on the 'master' branch Mar 3, 2020

Roel Janssen Reverting on the 'master' branch Mar 3, 2020

[Bioc-devel] Bioc2020: TODAY March 3rd is the last day to submit proposals for workshops/talks/posters

1 msg Mar 3

Shepherd, Lori Bioc2020: TODAY March 3rd is the last day to submit proposals for workshops/talks/posters Mar 3, 2020

[Bioc-devel] help: Adding a new branch with latest R version to package repository

2 msgs Mar 3

Selcen Arı help: Adding a new branch with latest R version to package repository Mar 3, 2020

Shepherd, Lori help: Adding a new branch with latest R version to package repository Mar 3, 2020

[Bioc-devel] Bioc2020 - Deadline for workshops/talk/poster TOMORROW

4 msgs Mar 2

Shepherd, Lori Bioc2020 - Deadline for workshops/talk/poster TOMORROW Mar 2, 2020

Simina Boca Bioc2020 - Deadline for workshops/talk/poster TOMORROW Mar 2, 2020

Levi Waldron Bioc2020 - Deadline for workshops/talk/poster TOMORROW Mar 2, 2020

Simina Boca Bioc2020 - Deadline for workshops/talk/poster TOMORROW Mar 2, 2020

[Bioc-devel] issue: maintainer of a Bioconductor package

1 msg Mar 2

Turaga, Nitesh issue: maintainer of a Bioconductor package Mar 2, 2020

Bioc-devel March 2020