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Bioc-devel April 2019

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Tuesday, April 30, 2019 12 emails
Martin Morgan package size issue Stephanie Gogarten check error in SeqVarTools Jianhai Zhang package size issue Hervé Pagès check error in SeqVarTools Turaga, Nitesh pushing changes to an existing package Simina Boca pushing changes to an existing package Shepherd, Lori check error in SeqVarTools Turaga, Nitesh Access to Bioconductor Git Credentials Shepherd, Lori Error: remote: error: hook declined to update refs/heads/RELEASE_3_8 Kaur Alasoo Error: remote: error: hook declined to update refs/heads/RELEASE_3_8 Dondelinger, Frank Access to Bioconductor Git Credentials Thomas Lawson Mc OSX fail [MSData::Spectrum::getMZIntensityPairs()] Sizes do not match
Monday, April 29, 2019 7 emails
Stephanie Gogarten check error in SeqVarTools Turaga, Nitesh RankProd package update Shepherd, Lori ensembl 96 gtfs and fasta twobits have been added to AnnotationHub Jianhong Ou, Ph.D. Error: invalid graphics state in creating vignettes Michael Lawrence When to use generics? Pages Gallego, M. When to use generics? Francesco Del Carratore RankProd package update
Sunday, April 28, 2019 5 emails
Leif Wigge R CMD check WARNING file link 'x' in package 'y' does not exist and so has been treated as a topic Tim Peters minfi::makeGenomicRatioSetFromMatrix() Windows mem alloc error Rainer Johannes Mc OSX fail [MSData::Spectrum::getMZIntensityPairs()] Sizes do not match Shin, Sunyoung Error: invalid graphics state in creating vignettes Thomas Lawson Mc OSX fail [MSData::Spectrum::getMZIntensityPairs()] Sizes do not match
Friday, April 26, 2019 12 emails
Aaron Lun Weird monkey identifiers in org.Hs.eg.db Zheng Wei 答复: package rJava can not be loaded in build system OS X Hervé Pagès package size issue Van Twisk, Daniel Weird monkey identifiers in org.Hs.eg.db Van Twisk, Daniel Fixes to db0s and org.db's + rebuild annotations depending on these Boris Steipe package size issue Jianhai Zhang package size issue Hervé Pagès EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9 Hu, Qiang EXTERNAL: Rcwl problems reported in the Multiple platform build/check report for BioC 3.9 Benjamin Tremblay R CMD check WARNING file link 'x' in package 'y' does not exist and so has been treated as a topic Shepherd, Lori Important Change to Release 3.9 Leif Wigge R CMD check WARNING file link 'x' in package 'y' does not exist and so has been treated as a topic
Thursday, April 25, 2019 9 emails
Hervé Pagès Weird monkey identifiers in org.Hs.eg.db Aaron Lun Weird monkey identifiers in org.Hs.eg.db Martin Morgan Error pushing changes for new package Hervé Pagès package rJava can not be loaded in build system OS X Hervé Pagès package rJava can not be loaded in build system OS X Shepherd, Lori package rJava can not be loaded in build system OS X Doug Barrows Error pushing changes for new package Zheng Wei package rJava can not be loaded in build system OS X Vincent Carey Weird monkey identifiers in org.Hs.eg.db
Wednesday, April 24, 2019 13 emails
Hervé Pagès build errors: "Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed" Martin Morgan How can I print a message on console with library("myPackage")? Hervé Pagès Unable to reproduce chimeraviz 3.9 build failure (test failure) Robert M. Flight How can I print a message on console with library("myPackage")? Stian Lågstad Unable to reproduce chimeraviz 3.9 build failure (test failure) Hervé Pagès No build report today (April 24, 2019) Arman Shahrisa How can I print a message on console with library("myPackage")? Hervé Pagès No build report today (April 24, 2019) Shepherd, Lori How can I print a message on console with library("myPackage")? Arman Shahrisa How can I print a message on console with library("myPackage")? Turaga, Nitesh failing package nucleoSim Shepherd, Lori Bioc 3.9 feature freeze Shepherd, Lori Managing Multiple GitHub Branches the Bioconductor Way
Tuesday, April 23, 2019 17 emails
Federico, Anthony, Nicholas Managing Multiple GitHub Branches the Bioconductor Way Hervé Pagès Release push DENIED by fallthru (REMP) Yinan Zheng Release push DENIED by fallthru (REMP) Hervé Pagès memory exhausted on tokay2 Taner Arslan Windows vignette build error "execution failed with error code 4" Jiefei Wang How can I print a message on console with library("myPackage")? Martin Morgan How can I print a message on console with library("myPackage")? Aaron Taudt memory exhausted on tokay2 Arman Shahrisa How can I print a message on console with library("myPackage")? Thomas Lin Pedersen Adding maintainer to mzID Turaga, Nitesh Adding maintainer to mzID Thomas Lin Pedersen Adding maintainer to mzID Paul Shannon build errors: "Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed" Van Twisk, Daniel Weird monkey identifiers in org.Hs.eg.db James W. MacDonald Weird monkey identifiers in org.Hs.eg.db Jianhong Ou, Ph.D. Error: invalid graphics state in creating vignettes Hervé Pagès build errors: "Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed"
Monday, April 22, 2019 4 emails
Shin, Sunyoung Error: invalid graphics state in creating vignettes Aaron Lun Weird monkey identifiers in org.Hs.eg.db Paul Shannon build errors: "Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed" Shepherd, Lori Important Release Deadlines This Week!!!
Sunday, April 21, 2019 1 email
Hervé Pagès celaya2: Warning: multiple methods tables found for rowSums
Friday, April 19, 2019 1 email
Ahmed Youssef celaya2: Warning: multiple methods tables found for rowSums
Thursday, April 18, 2019 10 emails
Junpeng Zhang How to change the name of R package that is already published on Bioconductor? Hervé Pagès How to change the name of R package that is already published on Bioconductor? Van Twisk, Daniel Community generated annotation deadline is April 24th Van Twisk, Daniel Bioconductor 3.9 Orgdbs and TxDbs available Hervé Pagès R CMD check testthat failure in tokay2 (devel branch) Marcel Ramos Dashes in GFF attributes Neumann, Steffen Help needed: Rdisop on Windows "File format not recognized" Martin Morgan Help needed: Rdisop on Windows "File format not recognized" Mike Smith Help needed: Rdisop on Windows "File format not recognized" Neumann, Steffen Help needed: Rdisop on Windows "File format not recognized"
Wednesday, April 17, 2019 3 emails
Valentino Giudice Dashes in GFF attributes Martin Morgan memory exhausted on tokay2 Hervé Pagès memory exhausted on tokay2
Tuesday, April 16, 2019 1 email
Hervé Pagès Packages with broken unit tests because of sample() change in R 3.6
Monday, April 15, 2019 7 emails
Hervé Pagès New build report Alina Selega New build report Hervé Pagès TIMEOUT and tokay2 require Rmpi Shepherd, Lori TIMEOUT and tokay2 require Rmpi Hamed Haseli Weird issue with the repo Hamed Haseli Weird issue with the repo Shepherd, Lori Last Day to commit to Release 3_8 branch
Sunday, April 14, 2019 5 emails
郝洁 TIMEOUT and tokay2 require Rmpi Hervé Pagès Pushing towards a better home for matrix generics Vincent Carey Help with installing netReg Spencer Brackett Help with installing netReg Martin Morgan GAlignments Constructor Type Checking Error
Saturday, April 13, 2019 8 emails
Hervé Pagès deprecation guidelines Hervé Pagès deprecation guidelines Dario Strbenac GAlignments Constructor Type Checking Error Hervé Pagès Windows-specific build error of 'seqCAT' package Hervé Pagès GWASTools error on tokay related to VariantAnnotation::readVcf Hervé Pagès New package submission failing only in devel due to dependent package errors Aaron Lun Problem with non-portable compiler flags on package test simo@e@tiberi m@iii@g oii uzh@ch Antwort: Re: TIMEOUTS in the submission systems
Friday, April 12, 2019 9 emails
Shepherd, Lori TIMEOUTS in the submission systems Bernat Gel TIMEOUTS in the submission systems Alina Selega New build report Shepherd, Lori New build report Alina Selega New build report Shepherd, Lori New build report Alina Selega New build report Martin Morgan Problem with non-portable compiler flags on package test Jochen Knaus Problem with non-portable compiler flags on package test
Thursday, April 11, 2019 10 emails
Steffi Grote loading database package changes random number Martin Morgan loading database package changes random number Hervé Pagès loading database package changes random number Martin Morgan loading database package changes random number Aaron Taudt memory exhausted on tokay2 Shepherd, Lori GWASTools error on tokay related to VariantAnnotation::readVcf Stephanie Gogarten GWASTools error on tokay related to VariantAnnotation::readVcf Samuela Pollack deprecation guidelines Steffi Grote loading database package changes random number Daniel Cameron New package submission failing only in devel due to dependent package errors
Wednesday, April 10, 2019 3 emails
Astrid Deschenes duplicate commits for nucleoSim margaret linan PoTRA building Man PDF Leonardo Collado Torres Packages with broken unit tests because of sample() change in R 3.6
Tuesday, April 9, 2019 9 emails
Benjamin Tremblay R CMD check testthat failure in tokay2 (devel branch) Michael Lawrence Pushing towards a better home for matrix generics Shepherd, Lori Final List of Deprecated Package Bioc 3.9 Peter Haverty Please un-deprecate gCrisprTools Van Twisk, Daniel Bioconductor 3.9 db0s are available Jurrian de Kanter "vdiffr" package load fail on celaya2 Hervé Pagès "vdiffr" package load fail on celaya2 Shepherd, Lori New package submission failing only in devel due to dependent package errors Daniel Cameron New package submission failing only in devel due to dependent package errors
Monday, April 8, 2019 14 emails
Hervé Pagès Packages with broken setClass statement Hervé Pagès Packages with broken unit tests because of sample() change in R 3.6 Martin Morgan git credentials Martin Morgan PoTRA function margaret linan PoTRA function Martin Morgan Version numbering rules and other policies Hervé Pagès Vignette Latex error Josef Spidlen Looking for a maintainer for the flowQB R/BioConductor package Karl Stamm Vignette Latex error Chengyang.Ji12 Version numbering rules and other policies Hannes Hettling git credentials cstrato celaya2 and merida2 are running different versions of R Shepherd, Lori Final List of Deprecated Package Bioc 3.9 Shepherd, Lori How to update my ssh keys (URGENT)
Sunday, April 7, 2019 4 emails
mohammed Elsiddieg How to update my ssh keys (URGENT) Hervé Pagès pandoc on celaya2 Hervé Pagès "vdiffr" package load fail on celaya2 Jurrian de Kanter "vdiffr" package load fail on celaya2
Saturday, April 6, 2019 5 emails
Hervé Pagès memory exhausted on tokay2 cstrato celaya2 and merida2 are running different versions of R Shepherd, Lori celaya2 and merida2 are running different versions of R cstrato celaya2 and merida2 are running different versions of R Aaron Taudt memory exhausted on tokay2
Friday, April 5, 2019 8 emails
Shepherd, Lori Deadline for devel branch 3.9 to pass R CMD build and R CMD check Shepherd, Lori celaya2 and merida2 are running different versions of R Samuela Pollack celaya2 and merida2 are running different versions of R Bernat Gel Timeout in check for a new submission Shepherd, Lori Timeout in check for a new submission Shepherd, Lori Timeout in check for a new submission Bernat Gel Timeout in check for a new submission Shepherd, Lori Package Submission Deadline is TODAY
Thursday, April 4, 2019 6 emails
Sarah Williams Intermittent ExperimentHub problems in vignette build Hervé Pagès Vignette Latex error Charles Joly ENCODExplorer: file size error Jayaram Kancherla error in bumphunter unit test (Shepherd, Lori) Shepherd, Lori ENCODExplorer: file size error Charles Joly ENCODExplorer: file size error
Wednesday, April 3, 2019 5 emails
Stephen Martin Pederson How to define S4 method for class from another package Martin Morgan How to define S4 method for class from another package Stephen Martin Pederson How to define S4 method for class from another package Martin Morgan How to define S4 method for class from another package Shepherd, Lori Vignette Latex error
Tuesday, April 2, 2019 10 emails
Stephen Martin Pederson How to define S4 method for class from another package Aaron Lun Call for collaborators/advice Karl Stamm Vignette Latex error Van Twisk, Daniel Bioconductor 3.9 contributed annotation package deadline Shepherd, Lori error in bumphunter unit test Samuela Pollack error in bumphunter unit test Martin Morgan Error when building BgeeCall package on Mac OS Shepherd, Lori Remaining windows build error Erik Fasterius Remaining windows build error Julien Wollbrett Error when building BgeeCall package on Mac OS
Monday, April 1, 2019 4 emails
Michael Lawrence DataFrame: replacement error Ludwig Geistlinger DataFrame: replacement error Shepherd, Lori Deadline for devel branch 3.9 to pass R CMD build and R CMD check Shepherd, Lori Deadline for commits to current Release 3.8 Branch