Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

Hi, Thank you for all the work in this transition Andrzej, Lori, Valerie, Nitesh and Hervé! I have a few questions about the new system. 1) I already had a github repo (that I manually kept in sync with the subversion one) for the recountWorkflow. Should I just follow the instructions at

Re: [Bioc-devel] Workflows are now in git (and other Important workflow-related changes)

For now the page at https://www.bioconductor.org/help/workflows/ will remain and be updated accordingly however there is discussion about having this page be removed or redirected. In the next few days I hope to have the new landing pages up and running and will make an announcement when

[Bioc-devel] AAString - Amino acid code enforced?

Dear all, probably this is for Hervé Pagès: I tried the following code, which should according to ?AAString not work, since ÜÖÄ are not part of any AA code. > AAString("ÜÄÖ") 3-letter "AAString" instance seq: ÜÄÖ > sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-w64-mingw32/x64

[Bioc-devel] Final List of Deprecated Packages for Bioc3.7

The Bioconductor Team has identified the following list of deprecated packages: Maintainer requested deprecation: Software Package: ontoCAT spliceR (functionalities moved to IsoformSwitchAnalyzeR) mvGST Experiment Data Package: RnaSeqTutorial cheung2010 MEALData (replaced with

[Bioc-devel] Release Deadline: Passing R CMD build and R CMD check

As stated in the release schedule The Deadline for all packages passing R CMD build and R CMD check without errors or warnings in devel is Wednesday April 25th. This includes software, data experiment and workflow packages. Some warnings will be accepted, with clarification on the bioc-devel

Re: [Bioc-devel] Need some help to submit a R package.

Hi, Please read through this documentation. http://bioconductor.org/developers/package-submission/ Nitesh > On Apr 2, 2018, at 2:00 AM, Pijush Das wrote: > > Dear Sir, > > > > I have developed an R package. I want to submit this package in > Bioconductor. > Please

[Bioc-devel] BiocGenerics::unique Bug? "Error: node stack overflow" in package esATAC

Dear all, I am a maintainer of package 'esATAC'. I find this error if calling library(rJava) before using BiocGenerics::unique. This error makes esATAC under bioc_3_7 check error because esATAC has to import rJava. The error reproduce-able code and session information is pasted below.

[Bioc-devel] Need some help to submit a R package.

Dear Sir, I have developed an R package. I want to submit this package in Bioconductor. Please help me to submit the R package. regards Pijush Das [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list

[Bioc-devel] Bioconductor New Package Submission Deadline Today!

Today is the final day to submit new packages to the Bioconductor contributions tracker to have a shot at being included in the upcoming 3.7 release at the end of the month. https://github.com/Bioconductor/Contributions Please note: submission today does not guarantee it will be included -

Re: [Bioc-devel] Error: node stack overflow

Hi Zheng, Thanks for the report. I will look into this and will let you know. H. On 04/01/2018 02:38 AM, Zheng Wei wrote: Dear all, I find this error if calling library(rJava) before using BiocGenerics::unique The code is pasted below. Thanks, Zheng > library(rJava) >

[Bioc-devel] Matrix::(cBind|rBind) to base::(cbind|rbind)

Hello Maintainers, The following packages have been identified for changing the functions ‘Matrix::cBind’ and ‘Matrix::rBind’ to the ‘base::cbind’ and ‘base::rbind’. The functions ‘Matrix::cBind’ and ‘Matrix::rBind’ have been deprecated by the author of the Matrix package.

Re: [Bioc-devel] Error: node stack overflow

I get the following on MacOSX, after library(rJava); library(GenomicRanges) -- take rJava out of the mix and there is no error. I ran into this originally as an interaction between rJava and Gviz, and have reported to Florian. That seemed to be MacOSX-specific. > gr1 <-

[Bioc-devel] Problem getting updated checkResults

Hi, I am trying to get the last version of my package(isomiRs) to be build by the testing system, but it seems it doesn’t get updated(http://bioconductor.org/checkResults/release/bioc-LATEST/isomiRs/). It is still seeing the version from last year even when I updated the package last week

[Bioc-devel] "convert" graphics error for new submission

for two host-types I am seeing an error that I do not know how to address Loading required package: ontologyIndex sh: line 1: 76907 Abort trap: 6 'convert' 'BiocOncoTK_files/figure-html/lkgbm-1.png' -trim 'BiocOncoTK_files/figure-html/lkgbm-1.png' > /dev/null sh: line 1: 76914 Abort

Re: [Bioc-devel] Problem getting updated checkResults

Yep, silly mistake, it seems I was in the stable version. Dummy me. I’ll kick myself for make you waste your time. Thanks for your time. > On Apr 2, 2018, at 5:30 PM, Obenchain, Valerie > wrote: > > Hi Lorena, > > You'll have to supply more information for

Re: [Bioc-devel] Problem getting updated checkResults

Hi Lorena, You'll have to supply more information for us to help you. The build report shows version 1.7.3: https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ What version are you expecting? Have you pushed all local changes to git.bioconductor.org? What does `git log` say? How

[Bioc-devel] BiocGenerics::unique Bug? Error: node stack overflow

Dear all, I am a maintainer of package 'esATAC' I find this error if calling library(rJava) before using BiocGenerics::unique The code is pasted below. Thanks, Zheng > library(rJava) > library(GenomicRanges) Loading required package: stats4 Loading required package: BiocGenerics Loading

Re: [Bioc-devel] Problem getting updated checkResults

No problem. I'm glad you figured it out. Valerie On 04/02/2018 03:16 PM, Lorena Pantano wrote: Yep, silly mistake, it seems I was in the stable version. Dummy me. I�ll kick myself for make you waste your time. Thanks for your time. On Apr 2, 2018, at 5:30 PM, Obenchain, Valerie

[Bioc-devel] Release of R package

Hi, I submitted R package MAGeCKFlute last year, which should be released recently. However, I checked the release list from " https://bioconductor.org/checkResults/release/bioc-LATEST/;, and I didn't find my package "MAGeCKFlute". Can you help to check that? And tell me why? Look forward for