Re: [Bioc-devel] Problem with GenomicFeatures::extractTranscriptSeqs

OK, seems we're getting closer - just updated all packages. Now the error is: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'windows' for signature '"DNAString"' my sessionInfo: > sessionInfo() R Under development (unstable) (2018-01-08

[Bioc-devel] GPos slower than GRanges ?

Hello, I have just discovered the GPos class, and I would like to use it in my "CAGEr" package, where for the moment I store single-nucleotide positions of transcription start sites in GRanges of width 1. But a simple microbenchmark sugests that, although GPos are more memory-efficient, they

Re: [Bioc-devel] error in loading pbdMPI on tokay2

On 02/08/2018 04:04 PM, Armen Abnousi wrote: Hi Martin, Thanks for your answer. What do you mean by "might go to the trouble of installing it", is there a way for us to install software on the build machines? I meant that individual users might install MPI, even if it were not installed

Re: [Bioc-devel] error in loading pbdMPI on tokay2

Hi Martin, Thanks for your answer. What do you mean by "might go to the trouble of installing it", is there a way for us to install software on the build machines? As for the other suggestion, I'm not sure whether using BiocFileCache::BiocFileCache() will be more efficient than using parallel

Re: [Bioc-devel] Updates not affected

So the release version was updated now. I guess it is affected with a bit of delay. Cheers! -- Ali Oghabian Bioinformatics, RNA-splicing laboratory (Room 4024B), Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki Finland. Email: ali.oghab...@helsinki.fi

Re: [Bioc-devel] Updates not affected

Thank you for the information. No actually I`m downloading the Bioc-devel now however I assume this is related to the devel version of the packages? How about the Release version? My git commits have not been affected in the release version either. Cheers, Ali -- Ali Oghabian

[Bioc-devel] Problem with GenomicFeatures::extractTranscriptSeqs

Dear all, one of the unit tests in ensembldb is failing because of a problem in GenomicFeatures::extractTranscriptSeqs (I guess): library(BSgenome.Hsapiens.NCBI.GRCh38) bsg <- BSgenome.Hsapiens.NCBI.GRCh38 library(EnsDb.Hsapiens.v86) all <- extractTranscriptSeqs(bsg, EnsDb.Hsapiens.v86) Error

Re: [Bioc-devel] Updates not affected

The website pages and build report are generated once a day. Once commits are made to the git.bioconductor.org repo it can take up to 24 hours to reflect on the website. Posting to the mailing list allows other on Bioconductor to chime in when appropriate. Cheers, Lori Shepherd

Re: [Bioc-devel] Updates not affected

remember that Bioconductor has _nightly_ builds, so commits today won't be reflected until tomorrow's build. See http://bioconductor.org/checkResults/ http://bioconductor.org/checkResults/3.7/bioc-LATEST/ http://bioconductor.org/checkResults/3.7/bioc-LATEST/IntEREst/malbec2-buildsrc.html

Re: [Bioc-devel] Updates not affected

Hi again! Ok, from now on I'll send to the email list. git remote -v origin https://github.com/gacatag/IntEREst.git (fetch) origin https://github.com/gacatag/IntEREst.git (push) upstreamg...@git.bioconductor.org:packages/IntEREst (fetch) upstream

Re: [Bioc-devel] Updates not affected

Hi Ali, Please send all these queries to the bioc-devel mailing list. There are other people on the team/developer community who can help you with these questions in the event there is no response from us. I need more information to check the your package, git remote -v (so that I

[Bioc-devel] Help with GWASTools

Hi, I am a graduate student at University of Texas School of Public health, and I am using GWASTools for the first time. I am trying to upload PLINK files to use, but I am getting an error which I cannot understand. I would appreciate if you could help me with the same. Code: bed.fn <-

Re: [Bioc-devel] error in loading pbdMPI on tokay2

On 02/07/2018 05:01 PM, Armen Abnousi wrote: Hi Valerie, Thanks for your reply. I can make it work using snow I believe. But the problem is that all functions in these packages that you have suggested (including snow; as far as I have seen) return the answer to one node and then if I want all

Re: [Bioc-devel] release build of ChemmineR failing

Dear Kevin, thank you for reporting the problem. It is not clear to me why do you need a Makefile to build your vignette in first place, could you maybe explain the motivation behind it? Cheers, Andrzej On Wed, Feb 7, 2018 at 5:37 PM, Kevin Horan wrote: > The

[Bioc-devel] release build of ChemmineR failing

The release version of ChemmineR is failing on windows. It seems to be a build script issue though, possibly something on your side. The package was building fine a few weeks ago and I have not modified it. Can you please have a look? Thanks. "C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/Rscript" -e