Bioc-devel October 2018

Activating account

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7 msgs · Oct 31 – Oct 31

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Lan Huong Nguyen Activating account Oct 31, 2018

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Martin Morgan Activating account Oct 31, 2018

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Lan Huong Nguyen Activating account Oct 31, 2018

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Martin Morgan Activating account Oct 31, 2018

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Lan Huong Nguyen Activating account Oct 31, 2018

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Martin Morgan Activating account Oct 31, 2018

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Lan Huong Nguyen Activating account Oct 31, 2018

Ascona Workshop 2019 -- Statistical Challenges in Medical Data Science, 16–21 June 2019

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1 msg · Oct 25

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Wolfgang Huber Ascona Workshop 2019 -- Statistical Challenges in Medical Data Science, 16–21 June 2019 Oct 25, 2018

Bad version number have been corrected for the following packages

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1 msg · Oct 1

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Turaga, Nitesh Bad version number have been corrected for the following packages Oct 1, 2018

BioC 3.8 build Error

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5 msgs · Oct 17 – Oct 17

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Martin, Patrick C N BioC 3.8 build Error Oct 17, 2018

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Shepherd, Lori BioC 3.8 build Error Oct 17, 2018

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Martin, Patrick C N BioC 3.8 build Error Oct 17, 2018

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Vincent Carey BioC 3.8 build Error Oct 17, 2018

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Martin, Patrick C N BioC 3.8 build Error Oct 17, 2018

BioC2019 June 24-27 in New York City

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1 msg · Oct 26

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Levi Waldron BioC2019 June 24-27 in New York City Oct 26, 2018

Bioc 3.8 feature freeze

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1 msg · Oct 24

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Obenchain, Valerie Bioc 3.8 feature freeze Oct 24, 2018

Bioc 3.8 packages: if/while condition

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2 msgs · Oct 15 – Oct 15

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Obenchain, Valerie Bioc 3.8 packages: if/while condition Oct 15, 2018

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Obenchain, Valerie Bioc 3.8 packages: if/while condition Oct 15, 2018

Bioconductor 3.8 OrgDb and TxDb packages now availiable

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1 msg · Oct 19

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Van Twisk, Daniel Bioconductor 3.8 OrgDb and TxDb packages now availiable Oct 19, 2018

Bioconductor 3.8 branch created

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1 msg · Oct 30

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Obenchain, Valerie Bioconductor 3.8 branch created Oct 30, 2018

Bioconductor 3.8 branching today

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1 msg · Oct 30

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Obenchain, Valerie Bioconductor 3.8 branching today Oct 30, 2018

Bioconductor 3.8 db0 annotation packages availiable; new deadline for contributed annotations Oct 22nd

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1 msg · Oct 14

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Van Twisk, Daniel Bioconductor 3.8 db0 annotation packages availiable; new deadline for contributed annotations Oct 22nd Oct 14, 2018

Bioconductor 3.8 is released

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1 msg · Oct 31

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Obenchain, Valerie Bioconductor 3.8 is released Oct 31, 2018

Bioconductor build still has not completed

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4 msgs · Oct 16 – Oct 16

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Koustav Pal Bioconductor build still has not completed Oct 16, 2018

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Shepherd, Lori Bioconductor build still has not completed Oct 16, 2018

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Koustav Pal Bioconductor build still has not completed Oct 16, 2018

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Shepherd, Lori Bioconductor build still has not completed Oct 16, 2018

Bioconductor package build fails

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4 msgs · Oct 11 – Oct 11

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Hoffman, Gabriel Bioconductor package build fails Oct 11, 2018

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Hervé Pagès Bioconductor package build fails Oct 11, 2018

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Hoffman, Gabriel Bioconductor package build fails Oct 11, 2018

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Martin Morgan Bioconductor package build fails Oct 11, 2018

Changing a name of a package already under review

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5 msgs · Oct 22 – Oct 25

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Lan Huong Nguyen Changing a name of a package already under review Oct 22, 2018

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Turaga, Nitesh Changing a name of a package already under review Oct 22, 2018

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Hervé Pagès Changing a name of a package already under review Oct 22, 2018

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Shepherd, Lori Changing a name of a package already under review Oct 23, 2018

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Lan Huong Nguyen Changing a name of a package already under review Oct 25, 2018

Contiributed annotations deadline

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1 msg · Oct 1

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Van Twisk, Daniel Contiributed annotations deadline Oct 1, 2018

Creating Bioconductor 3.8 branch on Oct 30

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1 msg · Oct 29

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Obenchain, Valerie Creating Bioconductor 3.8 branch on Oct 30 Oct 29, 2018

Deadline for Bioconductor packages to pass R CMD build/check

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1 msg · Oct 22

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Shepherd, Lori Deadline for Bioconductor packages to pass R CMD build/check Oct 22, 2018

Deadline for commits to current Release 3.7 Branch

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1 msg · Oct 1

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Shepherd, Lori Deadline for commits to current Release 3.7 Branch Oct 1, 2018

Deadline for devel branch 3.8 to pass R CMD build and R CMD check

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1 msg · Oct 1

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Shepherd, Lori Deadline for devel branch 3.8 to pass R CMD build and R CMD check Oct 1, 2018

Dependency to PEER

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1 msg · Oct 1

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Christian Mertes Dependency to PEER Oct 1, 2018

Error building the vignette

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2 msgs · Oct 25 – Oct 25

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Lluís Revilla Error building the vignette Oct 25, 2018

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Martin Morgan Error building the vignette Oct 25, 2018

Failed to update release 3_7

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2 msgs · Oct 20 – Oct 20

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Eugenia Galeota Failed to update release 3_7 Oct 20, 2018

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Shepherd, Lori Failed to update release 3_7 Oct 20, 2018

Failing GenVisR package

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2 msgs · Oct 22 – Oct 23

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Skidmore, Zach Failing GenVisR package Oct 22, 2018

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Obenchain, Valerie Failing GenVisR package Oct 23, 2018

Failure of IPAC package during check on Windows machine

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2 msgs · Oct 4 – Oct 4

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Gregory Ryslik Failure of IPAC package during check on Windows machine Oct 4, 2018

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Shepherd, Lori Failure of IPAC package during check on Windows machine Oct 4, 2018

Files in the 'vignettes' directory but no files in 'inst/doc'

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2 msgs · Oct 10 – Oct 10

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Bohdan Khomtchouk Files in the 'vignettes' directory but no files in 'inst/doc' Oct 10, 2018

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Martin Morgan Files in the 'vignettes' directory but no files in 'inst/doc' Oct 10, 2018

Have trouble in push to master branch

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6 msgs · Oct 11 – Oct 11

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Jianhong Ou, Ph.D. Have trouble in push to master branch Oct 11, 2018

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Turaga, Nitesh Have trouble in push to master branch Oct 11, 2018

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Zhu, Lihua (Julie) Have trouble in push to master branch Oct 11, 2018

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Turaga, Nitesh Have trouble in push to master branch Oct 11, 2018

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Jianhong Ou, Ph.D. Have trouble in push to master branch Oct 11, 2018

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Zhu, Lihua (Julie) Have trouble in push to master branch Oct 11, 2018

How to extend nonstandardGenericFunction

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5 msgs · Oct 19 – Oct 19

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Elizabeth Purdom How to extend nonstandardGenericFunction Oct 19, 2018

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Elizabeth Purdom How to extend nonstandardGenericFunction Oct 19, 2018

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Martin Morgan How to extend nonstandardGenericFunction Oct 19, 2018

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Elizabeth Purdom How to extend nonstandardGenericFunction Oct 19, 2018

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Elizabeth Purdom How to extend nonstandardGenericFunction Oct 19, 2018

Invalid Parameter - /figure-html

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2 msgs · Oct 9 – Oct 10

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Obenchain, Valerie Invalid Parameter - /figure-html Oct 9, 2018

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Obenchain, Valerie Invalid Parameter - /figure-html Oct 10, 2018

Issue with 'configure' not being executable

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6 msgs · Oct 29 – Oct 29

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Thomas Sherman Issue with 'configure' not being executable Oct 29, 2018

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Thomas Sherman Issue with 'configure' not being executable Oct 29, 2018

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Martin Morgan Issue with 'configure' not being executable Oct 29, 2018

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Thomas Sherman Issue with 'configure' not being executable Oct 29, 2018

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Martin Morgan Issue with 'configure' not being executable Oct 29, 2018

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Thomas Sherman Issue with 'configure' not being executable Oct 29, 2018

Last build of Bioconductor 3.7

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2 msgs · Oct 15 – Oct 15

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Obenchain, Valerie Last build of Bioconductor 3.7 Oct 15, 2018

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Turaga, Nitesh Last build of Bioconductor 3.7 Oct 15, 2018

Last day to commit changes to devel 3.8 branch and update NEWS file

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1 msg · Oct 22

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Shepherd, Lori Last day to commit changes to devel 3.8 branch and update NEWS file Oct 22, 2018

Last day to update NEWS files

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2 msgs · Oct 29 – Oct 29

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Shepherd, Lori Last day to update NEWS files Oct 29, 2018

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Shepherd, Lori Last day to update NEWS files Oct 29, 2018

Need update access agaisnt package 'banocc'

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11 msgs · Oct 17 – Oct 30

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George Weingart Need update access agaisnt package 'banocc' Oct 17, 2018

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Obenchain, Valerie Need update access agaisnt package 'banocc' Oct 17, 2018

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George Weingart Need update access agaisnt package 'banocc' Oct 17, 2018

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Turaga, Nitesh Need update access agaisnt package 'banocc' Oct 17, 2018

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Turaga, Nitesh Need update access agaisnt package 'banocc' Oct 18, 2018

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George Weingart Need update access agaisnt package 'banocc' Oct 18, 2018

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Turaga, Nitesh Need update access agaisnt package 'banocc' Oct 18, 2018

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George Weingart Need update access agaisnt package 'banocc' Oct 19, 2018

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Dario Strbenac Need update access agaisnt package 'banocc' Oct 20, 2018

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George Weingart Need update access agaisnt package 'banocc' Oct 29, 2018

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Shepherd, Lori Need update access agaisnt package 'banocc' Oct 30, 2018

New Feature: Ability to control pre-receive hooks in a modular way is active

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1 msg · Oct 11

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Turaga, Nitesh New Feature: Ability to control pre-receive hooks in a modular way is active Oct 11, 2018

New package: 0.99.x -> 1.0.0 ?

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2 msgs · Oct 26 – Oct 26

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André Veríssimo New package: 0.99.x -> 1.0.0 ? Oct 26, 2018

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Shepherd, Lori New package: 0.99.x -> 1.0.0 ? Oct 26, 2018

Only one week left to apply for the Better Scientific Software Fellowship program!

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1 msg · Oct 9

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Davis, Sean (NIH/NCI) [E] Only one week left to apply for the Better Scientific Software Fellowship program! Oct 9, 2018

Package Submission Deadline is TODAY!!

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1 msg · Oct 5

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Shepherd, Lori Package Submission Deadline is TODAY!! Oct 5, 2018

Package simulatorZ timeout under Windows on the release but not the devel branch

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2 msgs · Oct 9 – Oct 11

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Yuqing Zhang Package simulatorZ timeout under Windows on the release but not the devel branch Oct 9, 2018

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Obenchain, Valerie Package simulatorZ timeout under Windows on the release but not the devel branch Oct 11, 2018

Problem with setClassUnion and DelayedArray

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4 msgs · Oct 10 – Oct 11

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Elizabeth Purdom Problem with setClassUnion and DelayedArray Oct 10, 2018

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Michael Lawrence Problem with setClassUnion and DelayedArray Oct 10, 2018

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Hervé Pagès Problem with setClassUnion and DelayedArray Oct 10, 2018

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Elizabeth Purdom Problem with setClassUnion and DelayedArray Oct 11, 2018

RnBeads 2.0

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2 msgs · Oct 23 – Oct 23

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Fabian Müller RnBeads 2.0 Oct 23, 2018

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Hervé Pagès RnBeads 2.0 Oct 23, 2018

Roxygen documentation under windows

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4 msgs · Oct 7 – Oct 10

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Christian Mertes Roxygen documentation under windows Oct 7, 2018

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Shepherd, Lori Roxygen documentation under windows Oct 8, 2018

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Leonardo Collado Torres Roxygen documentation under windows Oct 8, 2018

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Christian Mertes Roxygen documentation under windows Oct 10, 2018

Rstudio returns fail for package check

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1 msg · Oct 1

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Arman Shahrisa Rstudio returns fail for package check Oct 1, 2018

Updated db0 packages available

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1 msg · Oct 19

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Van Twisk, Daniel Updated db0 packages available Oct 19, 2018

Why bioconductor?

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6 msgs · Oct 10 – Oct 11

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Ludwig Geistlinger Why bioconductor? Oct 10, 2018

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Levi Waldron Why bioconductor? Oct 10, 2018

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Turaga, Nitesh Why bioconductor? Oct 10, 2018

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Levi Waldron Why bioconductor? Oct 10, 2018

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Martin Morgan Why bioconductor? Oct 10, 2018

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Lluís Revilla Why bioconductor? Oct 11, 2018

Windows error "UCSC library operation failed" in package karyoploteR

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2 msgs · Sep 30 – Oct 1

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Dario Strbenac Windows error "UCSC library operation failed" in package karyoploteR Sep 30, 2018

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Bernat Gel Windows error "UCSC library operation failed" in package karyoploteR Oct 1, 2018

a pattern to be avoided? mcols(x)$y <- z

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2 msgs · Oct 3 – Oct 3

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Vincent Carey a pattern to be avoided? mcols(x)$y <- z Oct 3, 2018

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Hervé Pagès a pattern to be avoided? mcols(x)$y <- z Oct 3, 2018

avoiding circular dependencies between a Data package and a Software package

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8 msgs · Oct 6 – Oct 9

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Tim Triche, Jr. avoiding circular dependencies between a Data package and a Software package Oct 6, 2018

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Michael Lawrence avoiding circular dependencies between a Data package and a Software package Oct 6, 2018

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Obenchain, Valerie avoiding circular dependencies between a Data package and a Software package Oct 7, 2018

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Obenchain, Valerie avoiding circular dependencies between a Data package and a Software package Oct 7, 2018

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Shepherd, Lori avoiding circular dependencies between a Data package and a Software package Oct 8, 2018

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Tim Triche, Jr. avoiding circular dependencies between a Data package and a Software package Oct 8, 2018

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Obenchain, Valerie avoiding circular dependencies between a Data package and a Software package Oct 9, 2018

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Tim Triche, Jr. avoiding circular dependencies between a Data package and a Software package Oct 9, 2018

cTRAP: WARNINGS in package submission

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2 msgs · Oct 9 – Oct 9

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Nuno Agostinho cTRAP: WARNINGS in package submission Oct 9, 2018

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Shepherd, Lori cTRAP: WARNINGS in package submission Oct 9, 2018

change the codes in Bio

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2 msgs · Oct 23 – Oct 23

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Irene Zeng change the codes in Bio Oct 23, 2018

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Martin Morgan change the codes in Bio Oct 23, 2018

ensembl 94 gtfs and fasta twobits have been added to AnnotationHub

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1 msg · Oct 16

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Shepherd, Lori ensembl 94 gtfs and fasta twobits have been added to AnnotationHub Oct 16, 2018

how can I declare that a package doesn't/can't fully support Windows

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8 msgs · Oct 10 – Oct 12

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Tim Triche, Jr. how can I declare that a package doesn't/can't fully support Windows Oct 10, 2018

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Martin Morgan how can I declare that a package doesn't/can't fully support Windows Oct 10, 2018

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Hervé Pagès how can I declare that a package doesn't/can't fully support Windows Oct 10, 2018

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Hervé Pagès how can I declare that a package doesn't/can't fully support Windows Oct 10, 2018

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Tim Triche, Jr. how can I declare that a package doesn't/can't fully support Windows Oct 11, 2018

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Hervé Pagès how can I declare that a package doesn't/can't fully support Windows Oct 11, 2018

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Tim Triche, Jr. how can I declare that a package doesn't/can't fully support Windows Oct 12, 2018

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Hervé Pagès how can I declare that a package doesn't/can't fully support Windows Oct 12, 2018

query regarding bfg on bioconductor repository

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1 msg · Oct 31

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Turaga, Nitesh query regarding bfg on bioconductor repository Oct 31, 2018

write.table() of DataFrame introduces \n linebreaks in CSV output

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1 msg · Oct 24

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Neumann, Steffen write.table() of DataFrame introduces \n linebreaks in CSV output Oct 24, 2018