Re: [Rd] R Compilation gets stuck on Windows 64

Hi Avraham, A quick question - I realized I did not have *Perl* installed. So I installed *ActiveState Perl* right now. Also I see I need *texinfo* and *texi2any*. I was able to installed *texinfo* from here: http://gnuwin32.sourceforge.net/packages/texinfo.htm. But not sure where to get

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

Re: [Rd] R Compilation gets stuck on Windows 64

Hi Avraham, What a coincidence, I have been following this post of yours: https://www.avrahamadler.com/2013/10/24/an-openblas-based-rblas-for-windows-64-step-by-step/ Looks like this post is slightly older than what you have shared previously. It is strange that you did not get the attachments.

Re: [Rd] R Compilation gets stuck on Windows 64

On Thu, Feb 8, 2018 at 9:44 PM, Indrajit Sen Gupta wrote: > Hi All, > > I am trying to compile R from source on a 64 bit Windows. [snip] > I had compiled earlier with MinGW and had created the file: > *libopenblas_haswell-r0.2.20.a. * Hello, Indrajit. I don't see your

[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: [R-pkg-devel] R-devel warning: You used a knitr feature that depends on the digest package.

On 7 February 2018 at 15:03, luke-tier...@uiowa.edu wrote: | The problem is that this is an indirect dependency with knitr needing | digest and codetools to implement a feature (cacheing) that is being | asked for. And there is no obvious way (to me at least) of finding out | that these are

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

Re: [R-pkg-devel] [FORGED] Re: Depreciate Function

On 08/02/18 07:49, Rami Krispin wrote: I follow the example of the R Packages book about depreciating a function It would be helpful if you were to distinguish between the words "deprecate" and "depreciate". They are *VERY* different words. cheers, Rolf Turner -- Technical Editor

[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: [R-pkg-devel] Depreciate Function

Thanks for all the answers, I modified it to print function and it fixed the problem. Best regards, Rami Krispin On Wed, Feb 7, 2018 at 3:44 PM, William Dunlap wrote: > Instead of help(oldFunction) giving the example > oldFunction(x = something, option = "XYZ") > show

Re: [Rd] Warning from Sys.junction when using network drive.

Unfortunately, junctions cannot link to a network drive, they only can link directories on the same computer (possibly on different local volumes). This is a limitation imposed by Windows. I have updated the documentation for Sys.junction in R-devel accordingly. Tomas On 02/06/2018 10:50

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: [Rd] sparse.model.matrix Generates Non-Existent Factor Levels if Ord.factor Columns Present

color and clarity are ordered factors, so sparse.model.matrix is generating orthogonal-polynomial contrasts (see ?contr.poly). This is by design ... what are you trying to do? Are you interested in fac2sparse? On 18-02-07 11:00 PM, Dario Strbenac wrote: > Good day, > > Sometimes,

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