Bioc-devel - April 2018 - Date View

Monday, April 30, 2018 31 emails

Sunday, April 29, 2018 13 emails

Michael Lawrence Error: node stack overflow Peter Hickey bsseqData Hervé Pagès Error: node stack overflow Obenchain, Valerie bsseqData Peter Hickey bsseqData Peter Hickey Switch to SSH protocol for git clone instructions on package landing pages? Turaga, Nitesh Switch to SSH protocol for git clone instructions on package landing pages? Joris Meys Switch to SSH protocol for git clone instructions on package landing pages? Turaga, Nitesh bsseqData Peter Hickey bsseqData Peter Hickey Switch to SSH protocol for git clone instructions on package landing pages? Turaga, Nitesh bsseqData Peter Hickey bsseqData

Saturday, April 28, 2018 2 emails

Obenchain, Valerie bsseqData Kasper Daniel Hansen bsseqData

Friday, April 27, 2018 21 emails

H. Paul Benton bplapply - memory issue Radu Zabet DMRcaller build error Hervé Pagès DMRcaller build error Radu Zabet DMRcaller build error Hervé Pagès build machines Hervé Pagès DMRcaller build error Martin Morgan build machines Ludwig Geistlinger build machines Shepherd, Lori Build Error processing vignette Kucukural, Alper Build Error processing vignette Hervé Pagès How to update R version in terminal? Yuande Tan How to update R version in terminal? Shepherd, Lori Prostar problems reported in the Multiple platform build/check report for BioC 3.7 Samuel Wieczorek Prostar problems reported in the Multiple platform build/check report for BioC 3.7 Kasper Daniel Hansen build machines Pijush Das Need some help to submit a R package. Shepherd, Lori Need some help to submit a R package. Shepherd, Lori DEADLINE: commits to Bioc 3.7 Pijush Das Need some help to submit a R package. Shepherd, Lori Need some help to submit a R package. Pijush Das Need some help to submit a R package.

Thursday, April 26, 2018 16 emails

Hervé Pagès build machines Adrian Altenhoff Process to rename a bioconductor package Obenchain, Valerie No Mac builds for 3.7 today Diogo FT Veiga build machines Turaga, Nitesh Process to rename a bioconductor package Rahmatallah, Yasir BioC 3.7 Windows check warning "file link zz in package yy does not exist " Rahmatallah, Yasir BioC 3.7 Windows check warning "file link zz in package yy does not exist " Shepherd, Lori Errors on DAPAR and Prostar packages ?? Adrian Altenhoff Process to rename a bioconductor package Kasper Daniel Hansen build machines Shepherd, Lori Errors on DAPAR and Prostar packages ?? Samuel Wieczorek Errors on DAPAR and Prostar packages ?? Pariksheet Nanda Including data for @examples to run Shepherd, Lori BioC 3.7 Windows check warning "file link zz in package yy does not exist " Martin Morgan Need some help to submit a R package. Joris Meys BioC 3.7 Windows check warning "file link zz in package yy does not exist "

Wednesday, April 25, 2018 6 emails

Pijush Das Need some help to submit a R package. Rahmatallah, Yasir BioC 3.7 Windows check warning "file link zz in package yy does not exist " Paul Shannon dbApply name collision, RMySQL and RPostgreSQL, no direct call to either Valerie Obenchain Bioconductor 3.7 release candidate Adam Price Including data for @examples to run Shepherd, Lori Process to rename a bioconductor package

Tuesday, April 24, 2018 24 emails

Obenchain, Valerie Remove from email list Sara Linker Remove from email list Obenchain, Valerie " Error in serialize(data, node$con, xdr = FALSE)" during Vignette build (ChIC) Obenchain, Valerie Bioc 3.7 build failed for GenvisR package Obenchain, Valerie " Error in serialize(data, node$con, xdr = FALSE)" during Vignette build (ChIC) Karl Stamm git push confusion Shepherd, Lori Need some help to submit a R package. Shepherd, Lori biomaRt uswest mirror ERROR Mike Smith biomaRt uswest mirror ERROR Pijush Das Need some help to submit a R package. Alex Pico deleting irrelevant legacy objects from git repo? Shepherd, Lori biomaRt uswest mirror ERROR Turaga, Nitesh deleting irrelevant legacy objects from git repo? Alex Pico deleting irrelevant legacy objects from git repo? Turaga, Nitesh Failing package merhr Turaga, Nitesh deleting irrelevant legacy objects from git repo? campos vignette problems Martin Morgan vignette problems campos vignette problems Martin Morgan vignette problems Shepherd, Lori I could't push My package GMRP to github/master Shepherd, Lori Need some help to submit a R package. Pijush Das Need some help to submit a R package. campos vignette problems

Monday, April 23, 2018 21 emails

Hervé Pagès git push confusion Hervé Pagès problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment Turaga, Nitesh I could't push My package GMRP to github/master Turaga, Nitesh Unable to push to origin master Hervé Pagès dbApply name collision, RMySQL and RPostgreSQL, no direct call to either Giorgio Melloni Unable to push to origin master Turaga, Nitesh Unable to push to origin master Paul Shannon dbApply name collision, RMySQL and RPostgreSQL, no direct call to either Shepherd, Lori Deadline for All Package Maintainers Shepherd, Lori Deadline for All Package Maintainers Joris Meys Deadline for All Package Maintainers Turaga, Nitesh git push confusion Karl Stamm git push confusion Turaga, Nitesh git push confusion Karl Stamm git push confusion Turaga, Nitesh git push confusion Karl Stamm git push confusion Shepherd, Lori Warnind DaMiRseq Shepherd, Lori Deadline for All Package Maintainers Shepherd, Lori Process to rename a bioconductor package Mattia Chiesa Warnind DaMiRseq

Sunday, April 22, 2018 1 email

Alex Pico deleting irrelevant legacy objects from git repo?

Saturday, April 21, 2018 1 email

campos vignette problems

Friday, April 20, 2018 15 emails

Obenchain, Valerie build errors Ashish Jain Transition from Google Sheet to Web App Obenchain, Valerie build errors Obenchain, Valerie Transition from Google Sheet to Web App Ashish Jain Transition from Google Sheet to Web App Obenchain, Valerie Bioc 3.7 build failed for GenvisR package Shepherd, Lori package build error probably due to Biomart unavailability Blattmann Peter package build error probably due to Biomart unavailability Shepherd, Lori TIMEOUT on package MEAL Carlos Ruiz TIMEOUT on package MEAL Radu Zabet DMRcaller build error Shepherd, Lori Suggested edits to support site posting guide Sean Davis Subsetting Multiple platform build/check report Mike Smith Subsetting Multiple platform build/check report Kasper Daniel Hansen Subsetting Multiple platform build/check report

Thursday, April 19, 2018 14 emails

Leonardo Collado Torres Web App for SSH keys Obenchain, Valerie build errors Karl Stamm build errors Obenchain, Valerie Web App for SSH keys Adrian Altenhoff Process to rename a bioconductor package Leonardo Collado Torres Web App for SSH keys Obenchain, Valerie Transition from Google Sheet to Web App Marcel Ramos EXTERNAL: Fwd: [Bioconductor/Contributions] GIGSEA (#720) Lluís Revilla Transition from Google Sheet to Web App Martin Morgan Subsetting Multiple platform build/check report Neumann, Steffen Subsetting Multiple platform build/check report Shepherd, Lori ensembl 92 gtfs and fasta twobits have been added to AnnotationHub Shepherd, Lori GateFinder: Windows Server Error Ramon Diaz-Uriarte BioC 3.7 Windows check warning "file link zz in package yy does not exist "

Wednesday, April 18, 2018 18 emails

Shijia Zhu GIGSEA (#720) Tony Culos GateFinder: Windows Server Error Vincent Carey BioC 3.7 Windows check warning "file link zz in package yy does not exist " Martin Morgan BioC 3.7 Windows check warning "file link zz in package yy does not exist " Vincent Carey BioC 3.7 Windows check warning "file link zz in package yy does not exist " Turaga, Nitesh Transition from Google Sheet to Web App Martin, Tiphaine incompatibility between logo for build et the version and success of compilation Obenchain, Valerie Web App for SSH keys Shepherd, Lori incompatibility between logo for build et the version and success of compilation Martin, Tiphaine incompatibility between logo for build et the version and success of compilation Obenchain, Valerie Transition from Google Sheet to Web App Martin Morgan ‘SOCKcluster’ cluster error with bplapply() under merida2 Carmen M. Livi ‘SOCKcluster’ cluster error with bplapply() under merida2 Shepherd, Lori Can not push to bioconductor! please help me! Martin Morgan ‘SOCKcluster’ cluster error with bplapply() under merida2 Carmen M. Livi ‘SOCKcluster’ cluster error with bplapply() under merida2 Obenchain, Valerie Transition from Google Sheet to Web App Shepherd, Lori GateFinder: Windows Server Error

Tuesday, April 17, 2018 23 emails

Zhu MF Can not push to bioconductor! please help me! Tony Culos GateFinder: Windows Server Error Elizabeth Purdom problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment Ryan EXTERNAL: Accessing package citation info programmatically without running R? Ryan EXTERNAL: Accessing package citation info programmatically without running R? Marcel Ramos EXTERNAL: Accessing package citation info programmatically without running R? Van Twisk, Daniel TxDbs, OrgDbs, GO.db, and PFAM.db packages available Obenchain, Valerie Transition from Google Sheet to Web App Ryan Accessing package citation info programmatically without running R? Shepherd, Lori RareVariantVis failed Tomasz Stokowy RareVariantVis failed Shepherd, Lori RareVariantVis failed Tomasz Stokowy RareVariantVis failed Shepherd, Lori RareVariantVis failed Tomasz Stokowy RareVariantVis failed Elizabeth Purdom Problem with saveHDF5SummarizedExperiment in HDF5Array package Martin Morgan Problem with saveHDF5SummarizedExperiment in HDF5Array package Peter Hickey Problem with saveHDF5SummarizedExperiment in HDF5Array package Elizabeth Purdom Problem with saveHDF5SummarizedExperiment in HDF5Array package Mike Smith GIGSEA (#720) Carmen M. Livi GIGSEA (#720) Shijia Zhu GIGSEA (#720) Rainer Johannes Windows <Problems with Rd links to other packages on Tokay2>

Monday, April 16, 2018 20 emails

Marcel Ramos EXTERNAL: build_vignette Carmen M. Livi " Error in serialize(data, node$con, xdr = FALSE)" during Vignette build (ChIC) Giorgio Melloni Unable to push to origin master Shepherd, Lori Can not push to bioconductor! please help me! Turaga, Nitesh Can not push to bioconductor! please help me! Zhu MF Can not push to bioconductor! please help me! Ramon Diaz-Uriarte Windows <Problems with Rd links to other packages on Tokay2> Ramon Diaz-Uriarte BioC 3.7 Windows check warning "file link zz in package yy does not exist " Shepherd, Lori repository change after package acceptance Xu Qiao repository change after package acceptance Håkon Tjeldnes Windows <Problems with Rd links to other packages on Tokay2> Martin Morgan Need some help to submit a R package. Shepherd, Lori Windows <Problems with Rd links to other packages on Tokay2> Lluís Revilla repository change after package acceptance Mike Smith Windows <Problems with Rd links to other packages on Tokay2> Xu Qiao repository change after package acceptance Rainer Johannes Windows <Problems with Rd links to other packages on Tokay2> Mike Smith Windows <Problems with Rd links to other packages on Tokay2> Pijush Das Need some help to submit a R package. Rainer Johannes Windows <Problems with Rd links to other packages on Tokay2>

Sunday, April 15, 2018 9 emails

Ashish Jain "TissueEnrich" is missing in the BioC 3.7 build report Ruqian Lyu Need some help to submit a R package. Martin Morgan "TissueEnrich" is missing in the BioC 3.7 build report Ashish Jain "TissueEnrich" is missing in the BioC 3.7 build report Martin Morgan tokay2 error with httr Tomasz Stokowy RareVariantVis failed Klara Kaleb tokay2 error with httr Ruqian Lyu WARNING regarding imporing SummarizedExperiment Martin Morgan WARNING regarding imporing SummarizedExperiment

Saturday, April 14, 2018 7 emails

Ruqian Lyu WARNING regarding imporing SummarizedExperiment Ruqian Lyu WARNING regarding imporing SummarizedExperiment Michael Lawrence problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment Martin Morgan problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment Vincent Carey problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment Hervé Pagès Error: node stack overflow Hervé Pagès problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

Friday, April 13, 2018 15 emails

Hervé Pagès AAString - Amino acid code enforced? Tony Culos GateFinder Write Permission Leonardo Collado Torres Workflows are now in git (and other Important workflow-related changes) Turaga, Nitesh Bioconductor Git Access: GateFinder Turaga, Nitesh Bioconductor Git Access: GateFinder Turaga, Nitesh Bioconductor Git Access: GateFinder Turaga, Nitesh Bioconductor Git Access: GateFinder Tony Culos Bioconductor Git Access: GateFinder Shepherd, Lori TIMEOUT on package MEAL Paul Shannon right version "masked" by wrong version - not sure what "masked means" Shepherd, Lori right version "masked" by wrong version - not sure what "masked means" Shepherd, Lori Workflow Package Updates / Guidelines Carlos Ruiz TIMEOUT on package MEAL Shepherd, Lori commit not appearing in report Nicolas Descostes commit not appearing in report

Thursday, April 12, 2018 13 emails

Pijush Das Need some help to submit a R package. Michael Lawrence problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment Vincent Carey problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment Michael Lawrence problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment Davide Risso problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment Leonardo Collado Torres Suggested edits to support site posting guide Michael Lawrence problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment Aaron Lun problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment Obenchain, Valerie Setup for pushing changes in unifiedWMWqPCR to bioconductor git. Elizabeth Purdom problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment Michael Love Suggested edits to support site posting guide Obenchain, Valerie iGraph depending packages failing on Windows build machines Joris Meys Setup for pushing changes in unifiedWMWqPCR to bioconductor git.

Wednesday, April 11, 2018 18 emails

Kenneth Condon build_vignette Leonard Goldstein Bioc-devel changes and SummarizedExperiment class Turaga, Nitesh RELEASE_3_6 branch frozen at 3:00pm EST today Hervé Pagès update schedule of packages Turaga, Nitesh Unable to access repository Clare Pacini Unable to access repository Aimin Yan BiocCheck error Turaga, Nitesh Unable to access repository Minoo Ashtiani update schedule of packages campos vignette problems Martin Morgan vignette problems campos vignette problems Martin Morgan vignette problems campos vignette problems Obenchain, Valerie iGraph depending packages failing on Windows build machines Shepherd, Lori package is not available (for R version 3.4.4) Minoo Ashtiani package is not available (for R version 3.4.4) Elizabeth Purdom problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

Tuesday, April 10, 2018 21 emails

Obenchain, Valerie Mac builds in devel petr smirnov iGraph depending packages failing on Windows build machines Paul Shannon right version "masked" by wrong version - not sure what "masked means" Paul Shannon single-package build, from git trigger: new linux build report missing Martin Morgan single-package build, from git trigger: new linux build report missing Paul Shannon single-package build, from git trigger: new linux build report missing Martin Morgan BiocCheck error Paul Shannon single-package build, from git trigger: new linux build report missing Martin Morgan vignette problems Obenchain, Valerie Bioconductor 3.7 release: update NEWS Turaga, Nitesh RELEASE_3_6 branch frozen at 3:00pm EST tomorrow Aimin Yan BiocCheck error campos vignette problems Hervé Pagès Bioc-devel changes and SummarizedExperiment class Van Twisk, Daniel New db0 annotation packages Paul Shannon new package IGV needs web browsers on the build machines to pass build & check Sokratis Kariotis Update data in data package, pcxnData Clare Pacini Unable to access repository Stefan Haunsberger Update of miRBaseVersions.db annotation package Martin Morgan vignette problems campos vignette problems

Monday, April 9, 2018 10 emails

Vincent Carey new package IGV needs web browsers on the build machines to pass build & check Paul Shannon new package IGV needs web browsers on the build machines to pass build & check Vincent Carey new package IGV needs web browsers on the build machines to pass build & check Van Twisk, Daniel Update of miRBaseVersions.db annotation package Paul Shannon new package IGV needs web browsers on the build machines to pass build & check Martin Maechler BioC 3.7 Windows check warning "file link zz in package yy does not exist " Martin Morgan BioC 3.7 Windows check warning "file link zz in package yy does not exist " Ramon Diaz-Uriarte BioC 3.7 Windows check warning "file link zz in package yy does not exist " Martin Morgan vignette problems campos vignette problems

Sunday, April 8, 2018 1 email

Obenchain, Valerie Permission denied to Bioconductor repository

Saturday, April 7, 2018 1 email

Stefan Haunsberger Update of miRBaseVersions.db annotation package

Friday, April 6, 2018 8 emails

Van Twisk, Daniel Update of miRBaseVersions.db annotation package Zach Skidmore Bioc 3.7 build failed for GenvisR package Martin Morgan BioC 3.7 Windows check warning "file link zz in package yy does not exist " Ramon Diaz-Uriarte BioC 3.7 Windows check warning "file link zz in package yy does not exist " Lluís Revilla BioC 3.7 Windows check warning "file link zz in package yy does not exist " Vincent Carey BioC 3.7 Windows check warning "file link zz in package yy does not exist " Ramon Diaz-Uriarte BioC 3.7 Windows check warning "file link zz in package yy does not exist " Gabriela Merino Permission denied to Bioconductor repository

Thursday, April 5, 2018 13 emails

Vincent Carey "convert" graphics error for new submission Vincent Carey "convert" graphics error for new submission Alex Pico Big Changes for RCy3 v2.0.0 Martin Morgan "convert" graphics error for new submission Shepherd, Lori Update data in data package, pcxnData Stefan Haunsberger Update of miRBaseVersions.db annotation package Ramon Diaz-Uriarte BioC 3.7: build failing on Mac (merida2) because Cairo not available campos vignette problems Shepherd, Lori BioC 3.7: build failing on Mac (merida2) because Cairo not available Shepherd, Lori vignette problems Sokratis Kariotis Update data in data package, pcxnData campos vignette problems Shepherd, Lori Why my package has not been uploaded on bioc devel build list?

Wednesday, April 4, 2018 12 emails

Minoo Ashtiani Why my package has not been uploaded on bioc devel build list? Michael Lawrence problem in rbind with DelayedArray / HDF5Array package Elizabeth Purdom problem in rbind with DelayedArray / HDF5Array package Peter Hickey problem in rbind with DelayedArray / HDF5Array package Elizabeth Purdom problem in rbind with DelayedArray / HDF5Array package Gabriel Becker Missed deadline Paul Shannon web browser support missing in the build system? new package, IGV Kieran Campbell Tensorflow support for bioconductor packages Leonard Goldstein Bioc-devel changes and SummarizedExperiment class Ramon Diaz-Uriarte BioC 3.7: build failing on Mac (merida2) because Cairo not available Kasper Daniel Hansen Missed deadline Kenneth Condon Missed deadline

Tuesday, April 3, 2018 14 emails

Levi Waldron Missed deadline Gabriel Becker Missed deadline Levi Waldron Missed deadline Martin Morgan vignette problems Van Twisk, Daniel Bioconductor 3.7 annotation deadlines Shepherd, Lori Workflow package landing pages Robert Castelo RareVariantVis failed Aaron Lun Workflows are now in git (and other Important workflow-related changes) Shepherd, Lori Missed deadline Tomasz Stokowy RareVariantVis failed Andrzej Oleś Workflows are now in git (and other Important workflow-related changes) Kenneth Condon Missed deadline Mike Smith Release of R package Neumann, Steffen CfH: mzR 2.13.5 on macOS duplicated symbols from HDF5

Monday, April 2, 2018 18 emails

Watson Zhang Release of R package Obenchain, Valerie Problem getting updated checkResults Lorena Pantano Problem getting updated checkResults Obenchain, Valerie Problem getting updated checkResults Lorena Pantano Problem getting updated checkResults Vincent Carey "convert" graphics error for new submission Vincent Carey Error: node stack overflow Hervé Pagès Error: node stack overflow Turaga, Nitesh Matrix::(cBind|rBind) to base::(cbind|rbind) Shepherd, Lori Final List of Deprecated Packages for Bioc3.7 Leonardo Collado Torres Workflows are now in git (and other Important workflow-related changes) Felix Ernst AAString - Amino acid code enforced? Shepherd, Lori Release Deadline: Passing R CMD build and R CMD check Shepherd, Lori Bioconductor New Package Submission Deadline Today! Zheng Wei BiocGenerics::unique Bug? "Error: node stack overflow" in package esATAC Shepherd, Lori Workflows are now in git (and other Important workflow-related changes) Zheng Wei BiocGenerics::unique Bug? Error: node stack overflow Turaga, Nitesh Need some help to submit a R package.

Sunday, April 1, 2018 4 emails

Pijush Das Need some help to submit a R package. Martin Morgan vignette problems Martin Morgan vignette problems Aaron Lun Workflows are now in git (and other Important workflow-related changes)

Saturday, March 31, 2018 1 email

Gordon K Smyth No Windows binary for GenomicRanges

Bioc-devel April 2018