Re: [R-pkg-devel] How to remove rJava from Ecfun when it's not called directly or indirectly

On 2020-10-11 10:34, Enrico Schumann wrote: On Sat, 10 Oct 2020, Spencer Graves writes: Hello, All: "R CMD check Ecfun_0.2-4.tar.gz" fails under Windows 10 with "Error: package or namespace load failed for 'Ecfun': .onLoad failed in loadNamespace() for 'rJava'".

Re: [Rd] tools::package_dependencies problems

Have you tried using the 'db' argument to tools::package_dependencies? rbind the common columns of installed.packages() and available.packages() and use that as the package database. installed <- installed.packages() available <- available.packages() commonCols <-

Re: [Rd] tools::package_dependencies problems

Hi Spencer, You just need an available.packages matrix which reflects the reality you want to test against. There are probably various ways of getting one of these, but switchr allows you to build repositories off of many things including local directories, so you could do something like >

[Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'

This is more an R question than a Bioconductor question, but I would be grateful if the Biocore team or other Bioc developers have any insight. After upgrading to R 4.0.3 or R 4.1.0-devel, I find that running R CMD check under Windows now gives a worrying Note about .o files and 'abort'. The

[Rd] tools::package_dependencies problems

Hello, All: tools::package_dependencies('Ecfun') failed to find how my development version of Ecfun was using rJava, which generated errors in "R CMD build Ecfun". This is because package_dependencies by default uses CRAN and ignores locally installed packages. What do you think

[R-pkg-devel] Check: for detritus in the temp directory, Result: NOTE

I am trying to move the wrapr package from RUnit to tinytest. All seemed well on my tests, but when I submitted to CRAN I got: Flavor: r-devel-linux-x86_64-debian-gcc Check: for detritus in the temp directory, Result: NOTE Found the following files/directories: 'Rscript2be2.9jpLCF'

Re: [Bioc-devel] [EXTERNAL]Re: A question about r package update

Hi Kern, I checked the epihet on the website “bioconductor.org/packages/devel/bioc/html/epihet.html”. I saw its version is 1.5.2 Unfortunately, it is not the one I push this morning. It is not the latest one. Could you help me check what’s wrong here? I am so sorry about that. Best, Xiaowen

Re: [Bioc-devel] Package deprecation

Thank you for letting us know. We will take the necessary steps to deprecate the package. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

[Bioc-devel] Package deprecation

Dear Bioconductor core team, I have decided to retire metaArray package. Please remove the package before the next release. Thank you, Hyungwon -- Hyungwon Choi, Ph.D. Associate Professor Computational & Statistical Systems

[Bioc-devel] Bioconductor 3.12 db0s, OrgDbs and TxDbs now available

Hello Bioconductor Community! The newest db0s, OrgDbs, and TxDbs annotation packages for the upcoming Bioconductor 3.12 release are up and available for download in the devel version of Bioconductor. The deadline for submitting contributed annotations will be Wednesday October 21st. The new

Re: [Bioc-devel] A question about r package update

We apologize. It was announced on the Bioconductor slack but we forgot to post on the bioc-devel mailing list. There was an issue with the builders and there was no report generated yesterday Thursday October 15. The issue should be resolved and we expect a build report today. I do see 1.5.2

[Bioc-devel] A question about r package update

Hi bioc-devel, I am sorry for email you so often, this morning I checked the check report website, it did not change. And I noticed that the data is “This page was generated on 2020-10-14 11:07:41 -0400 (Wed, 14 Oct 2020).” Indeed I pushed my package on 2020-10-14. But its version is 1.5.2, not

Re: [Bioc-devel] Access g...@git.bioconductor.org:packages/Spectra.git

You have access now Laurent. Best regards, Nitesh On Oct 16, 2020, at 7:32 AM, Laurent Gatto mailto:laurent.ga...@uclouvain.be>> wrote: Dear Nitesh, Could you please grant me write access to g...@git.bioconductor.org:packages/Spectra.git. Johannes, who is