Bioc-devel May 2021

[Bioc-devel] Nominations for Bioconductor 2021 Awards

2 msgs May 28

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Shepherd, Lori Nominations for Bioconductor 2021 Awards May 24, 2021

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Shepherd, Lori Nominations for Bioconductor 2021 Awards May 28, 2021

[Bioc-devel] I don't have access to my package

2 msgs May 27

J

Jonathon Hill I don't have access to my package May 25, 2021

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Nitesh Turaga I don't have access to my package May 27, 2021

[Bioc-devel] About the size limitation of the package

6 msgs May 27

Y

You Zhou About the size limitation of the package May 26, 2021

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Shepherd, Lori About the size limitation of the package May 26, 2021

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Stuart Lee About the size limitation of the package May 26, 2021

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Vincent Carey About the size limitation of the package May 26, 2021

Y

You Zhou About the size limitation of the package May 27, 2021

Y

You Zhou About the size limitation of the package May 27, 2021

[Bioc-devel] C++ parallel computing

6 msgs May 26

O

Oleksii Nikolaienko C++ parallel computing May 24, 2021

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Martin Morgan C++ parallel computing May 25, 2021

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Oleksii Nikolaienko C++ parallel computing May 25, 2021

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Aaron Lun C++ parallel computing May 26, 2021

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Martin Morgan C++ parallel computing May 26, 2021

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Oleksii Nikolaienko C++ parallel computing May 26, 2021

[Bioc-devel] %outside% on GRanges

3 msgs May 26

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Oleksii Nikolaienko %outside% on GRanges May 26, 2021

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James W. MacDonald %outside% on GRanges May 26, 2021

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Oleksii Nikolaienko %outside% on GRanges May 26, 2021

[Bioc-devel] VariantAnnotation Installation Compile Error

6 msgs May 25

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Dario Strbenac VariantAnnotation Installation Compile Error May 23, 2021

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Vincent Carey VariantAnnotation Installation Compile Error May 24, 2021

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Dario Strbenac VariantAnnotation Installation Compile Error May 24, 2021

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Vincent Carey VariantAnnotation Installation Compile Error May 24, 2021

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Dario Strbenac VariantAnnotation Installation Compile Error May 24, 2021

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Dario Strbenac VariantAnnotation Installation Compile Error May 25, 2021

[Bioc-devel] RELEASE_3_13 is now available for bioconductor_docker

1 msg May 24

N

Nitesh Turaga RELEASE_3_13 is now available for bioconductor_docker May 24, 2021

[Bioc-devel] Access to schex

4 msgs May 21

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Saskia Freytag Access to schex May 15, 2021

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Nitesh Turaga Access to schex May 17, 2021

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Saskia Freytag Access to schex May 21, 2021

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Nitesh Turaga Access to schex May 21, 2021

[Bioc-devel] Bioconductor 3.14 R Version

2 msgs May 21

C

Chris Eeles Bioconductor 3.14 R Version May 21, 2021

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Shepherd, Lori Bioconductor 3.14 R Version May 21, 2021

[Bioc-devel] missing GenomicScores platform availability shield for release

2 msgs May 21

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Shepherd, Lori missing GenomicScores platform availability shield for release May 21, 2021

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Robert Castelo missing GenomicScores platform availability shield for release May 21, 2021

[Bioc-devel] EnMCB reduce dependencies

3 msgs May 21

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xin wwa EnMCB reduce dependencies May 21, 2021

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Vincent Carey EnMCB reduce dependencies May 21, 2021

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xin wwa EnMCB reduce dependencies May 21, 2021

[Bioc-devel] Bioconductor 3.13 is Released!

1 msg May 20

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Shepherd, Lori Bioconductor 3.13 is Released! May 20, 2021

[Bioc-devel] Bioconductor git repository commits have resumed

2 msgs May 19

N

Nitesh Turaga Bioconductor git repository commits have resumed May 19, 2021

N

Nitesh Turaga Bioconductor git repository commits have resumed May 19, 2021

[Bioc-devel] Creating Bioconductor 3.13 branch on May 19th 2021 - 11 AM EDT

1 msg May 19

N

Nitesh Turaga Creating Bioconductor 3.13 branch on May 19th 2021 - 11 AM EDT May 19, 2021

[Bioc-devel] genefu Warning

2 msgs May 18

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Eeles, Christopher genefu Warning May 18, 2021

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Marcel Ramos EXTERNAL: [BULK] genefu Warning May 18, 2021

[Bioc-devel] Last day to make commit before the RELEASE_3_13

5 msgs May 18

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Shepherd, Lori Last day to make commit before the RELEASE_3_13 May 18, 2021

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Martin, Tiphaine Last day to make commit before the RELEASE_3_13 May 18, 2021

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Fabricio de Almeida Last day to make commit before the RELEASE_3_13 May 18, 2021

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Shepherd, Lori Last day to make commit before the RELEASE_3_13 May 18, 2021

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Martin, Tiphaine Last day to make commit before the RELEASE_3_13 May 18, 2021

[Bioc-devel] MSstatsTMTPTM deprecation

2 msgs May 18

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Devon Kohler MSstatsTMTPTM deprecation May 18, 2021

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Shepherd, Lori MSstatsTMTPTM deprecation May 18, 2021

[Bioc-devel] XNAString landing page

3 msgs May 17

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Plucinska, Marianna XNAString landing page May 17, 2021

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Shepherd, Lori XNAString landing page May 17, 2021

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Shepherd, Lori XNAString landing page May 17, 2021

[Bioc-devel] MSstatsPTM Maintainer Change

2 msgs May 14

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Devon Kohler MSstatsPTM Maintainer Change May 12, 2021

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Nitesh Turaga MSstatsPTM Maintainer Change May 14, 2021

[Bioc-devel] AnnotationHub Corrupt Cache

2 msgs May 14

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Jeroen Gilis AnnotationHub Corrupt Cache May 14, 2021

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Shepherd, Lori AnnotationHub Corrupt Cache May 14, 2021

[Bioc-devel] Cannot reproduce "TeX capacity exceeded" error on build hosts (package messina)

2 msgs May 13

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Mark Pinese Cannot reproduce "TeX capacity exceeded" error on build hosts (package messina) May 13, 2021

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Hervé Pagès Cannot reproduce "TeX capacity exceeded" error on build hosts (package messina) May 13, 2021

[Bioc-devel] Transferring the maintainship of MSstatsPTM

2 msgs May 13

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Tsung-Heng Tsai Transferring the maintainship of MSstatsPTM May 12, 2021

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Devon Kohler Transferring the maintainship of MSstatsPTM May 13, 2021

[Bioc-devel] Problems while activating my bioconductor git account

3 msgs May 13

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Sebastian Bauer Problems while activating my bioconductor git account May 12, 2021

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Nitesh Turaga Problems while activating my bioconductor git account May 12, 2021

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Shepherd, Lori Problems while activating my bioconductor git account May 13, 2021

[Bioc-devel] Pipeline Structure in Package

1 msg May 12

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Matt Moravec Pipeline Structure in Package May 12, 2021

[Bioc-devel] Bioconductor AMI's

1 msg May 12

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Shepherd, Lori Bioconductor AMI's May 12, 2021

[Bioc-devel] Pushing changes to Bioconductor in a new machine

2 msgs May 12

F

Fabricio de Almeida Pushing changes to Bioconductor in a new machine May 12, 2021

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Shepherd, Lori Pushing changes to Bioconductor in a new machine May 12, 2021

[Bioc-devel] reproducing the BioC package error

2 msgs May 12

V

Venu Thatikonda reproducing the BioC package error May 12, 2021

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Vincent Carey reproducing the BioC package error May 12, 2021

[Bioc-devel] Install and check error in Windows without any relevant message

4 msgs May 12

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Ramon Diaz-Uriarte Install and check error in Windows without any relevant message May 11, 2021

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Ramon Diaz-Uriarte Install and check error in Windows without any relevant message May 11, 2021

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Hervé Pagès Install and check error in Windows without any relevant message May 11, 2021

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Ramon Diaz-Uriarte Install and check error in Windows without any relevant message May 12, 2021

[Bioc-devel] BFG clean-up and reset for compartmap

1 msg May 11

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Nitesh Turaga BFG clean-up and reset for compartmap May 11, 2021

[Bioc-devel] Maintainer change Bioconductor packages

3 msgs May 11

P

Pablo Moreno Maintainer change Bioconductor packages May 10, 2021

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Nitesh Turaga Maintainer change Bioconductor packages May 11, 2021

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Nitesh Turaga Maintainer change Bioconductor packages May 11, 2021

[Bioc-devel] BFG clean-up and reset for compartmap

4 msgs May 11

J

Johnson, Ben BFG clean-up and reset for compartmap May 10, 2021

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Nitesh Turaga BFG clean-up and reset for compartmap May 11, 2021

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Johnson, Ben BFG clean-up and reset for compartmap May 11, 2021

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Nitesh Turaga BFG clean-up and reset for compartmap May 11, 2021

[Bioc-devel] Transfer Maintainership of the Package NetSAM

3 msgs May 11

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Zhang, Bing Transfer Maintainership of the Package NetSAM May 9, 2021

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Zhang, Bing Transfer Maintainership of the Package NetSAM May 9, 2021

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Nitesh Turaga Transfer Maintainership of the Package NetSAM May 11, 2021

[Bioc-devel] CTCF AnnotationHub package

2 msgs May 10

M

Mikhail Dozmorov CTCF AnnotationHub package May 10, 2021

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Shepherd, Lori CTCF AnnotationHub package May 10, 2021

[Bioc-devel] Bioc 3.13 Feature Freeze and Deadline for passing R CMD build/check

2 msgs May 10

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Shepherd, Lori Bioc 3.13 Feature Freeze and Deadline for passing R CMD build/check May 10, 2021

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Shepherd, Lori Bioc 3.13 Feature Freeze and Deadline for passing R CMD build/check May 10, 2021

[Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

3 msgs May 10

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Neumann, Steffen Do we have an unpacked archive for BioC, so that we can URL link to individual files ? May 10, 2021

M

Mike Smith Do we have an unpacked archive for BioC, so that we can URL link to individual files ? May 10, 2021

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Martin Morgan Do we have an unpacked archive for BioC, so that we can URL link to individual files ? May 10, 2021

[Bioc-devel] Sudden Bioconductor nightly build fail for IsoCorrectoRGUI: cannnot add binding of 'variable' to the base environment

4 msgs May 9

C

Christian Kohler Sudden Bioconductor nightly build fail for IsoCorrectoRGUI: cannnot add binding of 'variable' to the base environment May 3, 2021

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Martin Morgan Sudden Bioconductor nightly build fail for IsoCorrectoRGUI: cannnot add binding of 'variable' to the base environment May 4, 2021

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Christian Kohler Sudden Bioconductor nightly build fail for IsoCorrectoRGUI: cannnot add binding of 'variable' to the base environment May 5, 2021

C

Christian Kohler Sudden Bioconductor nightly build fail for IsoCorrectoRGUI: cannnot add binding of 'variable' to the base environment May 9, 2021

[Bioc-devel] avoid updating BiocManager to 1.30.13; provisional fix available

1 msg May 8

V

Vincent Carey avoid updating BiocManager to 1.30.13; provisional fix available May 8, 2021

[Bioc-devel] Can't install Bioconductor 3.13 under Windows 10

2 msgs May 8

G

Gordon K Smyth Can't install Bioconductor 3.13 under Windows 10 May 8, 2021

V

Vincent Carey Can't install Bioconductor 3.13 under Windows 10 May 8, 2021

[Bioc-devel] Bioconductor 3.13 db0s, OrgDbs and TxDbs now available

1 msg May 7

I

Interdonato, Kayla Bioconductor 3.13 db0s, OrgDbs and TxDbs now available May 7, 2021

[Bioc-devel] Force Package Update after Removing Large Files from .git History

3 msgs May 6

G

Gabriel Odom Force Package Update after Removing Large Files from .git History May 5, 2021

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Nitesh Turaga Force Package Update after Removing Large Files from .git History May 6, 2021

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Gabriel Odom Force Package Update after Removing Large Files from .git History May 6, 2021

[Bioc-devel] Question about IRanges for coordinates greater than 536870912

1 msg May 6

J

Jianhong Ou, Ph.D. Question about IRanges for coordinates greater than 536870912 May 6, 2021

[Bioc-devel] How to repeat the error: shape of 'skeleton' is not compatible with 'NROW(flesh)'

3 msgs May 6

J

Jianhong Ou, Ph.D. How to repeat the error: shape of 'skeleton' is not compatible with 'NROW(flesh)' May 6, 2021

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Shepherd, Lori How to repeat the error: shape of 'skeleton' is not compatible with 'NROW(flesh)' May 6, 2021

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Jianhong Ou, Ph.D. How to repeat the error: shape of 'skeleton' is not compatible with 'NROW(flesh)' May 6, 2021

[Bioc-devel] Windows build. error: "DLL 'RcppParallel' not found: maybe not installed for this architecture?"

2 msgs May 6

S

stefano iacus Windows build. error: "DLL 'RcppParallel' not found: maybe not installed for this architecture?" May 5, 2021

S

Shepherd, Lori Windows build. error: "DLL 'RcppParallel' not found: maybe not installed for this architecture?" May 6, 2021

[Bioc-devel] Fixing build error for the first time

3 msgs May 5

F

Fabricio de Almeida Fixing build error for the first time May 5, 2021

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Shepherd, Lori Fixing build error for the first time May 5, 2021

F

Fabricio de Almeida Fixing build error for the first time May 5, 2021

[Bioc-devel] Maintainer for preciseTAD

2 msgs May 5

M

Mikhail Dozmorov Maintainer for preciseTAD May 4, 2021

N

Nitesh Turaga Maintainer for preciseTAD May 5, 2021

[Bioc-devel] Time-out error on Ubuntu 20.04 build

3 msgs May 5

S

Selles Vidal, Lara Time-out error on Ubuntu 20.04 build May 3, 2021

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Hervé Pagès Time-out error on Ubuntu 20.04 build May 3, 2021

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Selles Vidal, Lara Time-out error on Ubuntu 20.04 build May 5, 2021

[Bioc-devel] DENIED when update package EnMCB (hook declined)

2 msgs May 5

X

xin wwa DENIED when update package EnMCB (hook declined) May 5, 2021

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Shepherd, Lori DENIED when update package EnMCB (hook declined) May 5, 2021

[Bioc-devel] Log in to the BiocCredentials app

5 msgs May 4

M

mauro castro Log in to the BiocCredentials app May 4, 2021

N

Nitesh Turaga Log in to the BiocCredentials app May 4, 2021

M

mauro castro Log in to the BiocCredentials app May 4, 2021

N

Nitesh Turaga Log in to the BiocCredentials app May 4, 2021

M

mauro castro Log in to the BiocCredentials app May 4, 2021

[Bioc-devel] Can anyone reproduce this? Possible bug or typo in BiocManager:::.version_map() or upstream

2 msgs May 4

W

Wolfgang Huber Can anyone reproduce this? Possible bug or typo in BiocManager:::.version_map() or upstream May 4, 2021

M

Martin Morgan Can anyone reproduce this? Possible bug or typo in BiocManager:::.version_map() or upstream May 4, 2021

[Bioc-devel] Build error on Mac re: Arial font and polygon edges

1 msg May 4

S

Shraddha Pai Build error on Mac re: Arial font and polygon edges May 4, 2021

[Bioc-devel] Bioconductor Release Announcement: RELEASE_3_12 branch freeze

5 msgs May 4

N

Nitesh Turaga Bioconductor Release Announcement: RELEASE_3_12 branch freeze May 3, 2021

N

Nitesh Turaga Bioconductor Release Announcement: RELEASE_3_12 branch freeze May 3, 2021

N

Nitesh Turaga Bioconductor Release Announcement: RELEASE_3_12 branch freeze May 3, 2021

W

Waldir Leoncio Netto Bioconductor Release Announcement: RELEASE_3_12 branch freeze May 3, 2021

N

Nitesh Turaga Bioconductor Release Announcement: RELEASE_3_12 branch freeze May 4, 2021

[Bioc-devel] Cannot find my package "interacCircos" on check results of BioC3.13

2 msgs May 4

崔

崔哲 Cannot find my package "interacCircos" on check results of BioC3.13 May 3, 2021

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Shepherd, Lori Cannot find my package "interacCircos" on check results of BioC3.13 May 4, 2021

[Bioc-devel] Bioc Git credentials

3 msgs May 3

L

Leonard Goldstein Bioc Git credentials May 2, 2021

N

Nitesh Turaga Bioc Git credentials May 3, 2021

L

Leonard Goldstein Bioc Git credentials May 3, 2021

[Bioc-devel] issue with ssh public key

4 msgs May 3

M

Martin, Tiphaine issue with ssh public key May 1, 2021

N

Nitesh Turaga issue with ssh public key May 3, 2021

M

Martin, Tiphaine issue with ssh public key May 3, 2021

N

Nitesh Turaga issue with ssh public key May 3, 2021

[Bioc-devel] documentation of raw data

1 msg May 3

S

Shepherd, Lori documentation of raw data May 3, 2021

[Bioc-devel] Rd warnings in Windows bioc-devel check

2 msgs May 1

B

Benjamin Jean-Marie Tremblay Rd warnings in Windows bioc-devel check May 1, 2021

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Deepayan Sarkar Rd warnings in Windows bioc-devel check May 1, 2021