Re: [Bioc-devel] build errors: "Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed"

Hi Paul, Is there a possibility that trena's code is having one worker downloading/re-installing BSgenome.Hsapiens.UCSC.hg38 while at the same time another worker is trying to access it? The reason I suspect something like this is that it seems that BSgenome.Hsapiens.UCSC.hg38 gets

Re: [Bioc-devel] Release push DENIED by fallthru (REMP)

Hi Yinan, The RELEASE_3_8 branch was frozen 8 days ago. This was announced on this list: https://stat.ethz.ch/pipermail/bioc-devel/2019-April/014931.html Best, H. On 4/23/19 13:53, Yinan Zheng wrote: > Hi Bioc Devel Team, > > I fixed some bugs in my package REMP but failed to push the

[Bioc-devel] Release push DENIED by fallthru (REMP)

Hi Bioc Devel Team, I fixed some bugs in my package REMP but failed to push the changes to the release version (works fine to push to devel version and github). Would you please advise how should I fix it? (I have been following the same git code provided on the website previously and this

Re: [Bioc-devel] memory exhausted on tokay2

Glad you found the culprit. Actually, the use of data.table::fwrite() seems to cause a memory leak. More precisely, if I repeatedly run the full exportMethylome example in a terminal, the memory usage (reported by 'top' in another terminal) grows at a rate of 0.8 Gb per run. I observed this on

[Bioc-devel] Windows vignette build error "execution failed with error code 4"

Dear all, My package is almost ready to be accepted but now i am getting weird building error on Windows. It works without error on Linux and OS X. I have tried many many things. But I could not figured out. The error is: Invalid Parameter - /figure-html Warning in shell(paste(c(cmd, args),

Re: [Bioc-devel] memory exhausted on tokay2

Dear Hervé, thank you (and Martin) for the advice. I was able to locate the culprit: it was a data.table::fwrite( ) statement, the behaviour of which must have changed since the last release. I put this example in a NOT RUN block. Kind regards, Aaron Am Mi., 17. Apr. 2019 um 12:41 Uhr

Re: [Bioc-devel] How can I print a message on console with library("myPackage")?

This is called the 'tragedy of the commons', where everyone seems something that looks good (screen real-estate to advertise their package) and so takes advantage of it. Once everyone does that, the 'commons' is completely destroyed by messages like the one you're trying to suppress. You can

Re: [Bioc-devel] How can I print a message on console with library("myPackage")?

Hi Arman, I only have a suggestion for your first question, have you tried .onLoad functions? R will call it when loading the package using library(). You can put your message function in .onLoad. Best, Jiefei Arman Shahrisa 于2019年4月23日周二 下午3:04写道： > I’m the maintainer of package “cbaf”. I

Re: [Bioc-devel] Adding maintainer to mzID

Great - the description file should already reflect this. Thanks Thomas > On 23 Apr 2019, at 20.51, Turaga, Nitesh > wrote: > > Hi Thomas, > > You found the right place. Please issue the change on the package as well (in > the devel version), change the maintainer to Laurent Gatto. > >

Re: [Bioc-devel] Adding maintainer to mzID

Hi Thomas, You found the right place. Please issue the change on the package as well (in the devel version), change the maintainer to Laurent Gatto. Laurent should now have access to this package. Best regards, Nitesh > On Apr 23, 2019, at 2:46 PM, Thomas Lin Pedersen wrote: > > Hi > >

[Bioc-devel] Adding maintainer to mzID

Hi I wish to add Laurent Gatto as maintainer of the mzID package and give him full read/write rights to the repository. Is this the formal route for doing that? best Thomas ___ Bioc-devel@r-project.org mailing list

Re: [Bioc-devel] build errors: "Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed"

Hi Herve, Thanks for your reply! > Is there a possibility that trena's code is having one worker > downloading/re-installing BSgenome.Hsapiens.UCSC.hg38 while at the same > time another worker is trying to access it? I don’t think any download or reinstalling happens. Several genome packages

Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db

We've made some changes to our annotation generation scripts this release and it seems these may have introduced some errors. Thank you for identifying this issue and I will try to have some fixes out asap. From: Bioc-devel on behalf of James W. MacDonald

Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db

Looks like the ensembl table of the human.db0 package got polluted with *Pan troglodytes* genes: > con <- dbConnect(SQLite(), "/R-devel/lib64/R/library/human.db0/extdata/chipsrc_human.sqlite") > dbGetQuery(con, "select count(*) from ensembl where ensid like 'ENSPTR%';") count(*) 116207 >

Re: [Bioc-devel] Error: invalid graphics state in creating vignettes

Hi Sunyong, plotMotifLogo does not compatible with par now. Please use grid to plot the multiple panels in one canvas. I am working on this but it takes time. Jianhong. On 4/23/19, 12:47 AM, "Bioc-devel on behalf of Shin, Sunyoung" wrote: Dear all, I got an error message: