Re: [Bioc-devel] select(Homo.sapiens,...) failing

Thanks Val that did the trick. On Mon, May 2, 2016 at 4:40 PM, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Hi Vince, > > You need version >=1.13.9 of OrganismDbi. Unfortunately it's failing > check because of the biomart problems so you'll have to get it from svn. > Let me

Re: [Bioc-devel] How to debug for the warnings?

On 05/02/2016 05:53 PM, Ou, Jianhong wrote: Hi All, I got some warnings when check. However, I could not see any details for that warnings. How could I debug for these kind of warnings? Thank you. Please see this thread https://stat.ethz.ch/pipermail/bioc-devel/2016-May/009205.html and

Re: [Bioc-devel] some new warnings in a package

On 05/02/2016 12:37 PM, Ludwig Geistlinger wrote: So yes, you should update the NAMESPACE file following the warning message you see in your build report. Hi Martin, I did not encounter such a note on importing from base packages ever before - but ok, I followed your suggestion and added the

[Bioc-devel] How to debug for the warnings?

Hi All, I got some warnings when check. However, I could not see any details for that warnings. How could I debug for these kind of warnings? Thank you. * using log directory �/home/biocbuild/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck� * using R version 3.3.0 RC (2016-04-25 r70549) * using

Re: [Bioc-devel] select(Homo.sapiens,...) failing

Hi Vince, You need version >=1.13.9 of OrganismDbi. Unfortunately it's failing check because of the biomart problems so you'll have to get it from svn. Let me know if you still have problems after updating. Val On 05/02/2016 11:53 AM, Vincent Carey wrote: > biocValid() says all is well ... >

Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

Well, you can tell your helpdesk that this is going to impact people's work as the OS you are using will no longer be supported by R/Bioconductor starting with the release this week. Mavericks was released 3 years ago. It seems reasonable to support it now. Dan - Original Message - >

Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

Hi Dan, Thank you for your answer. I hope I can update to Mavericks but our help desk just ask me to hold on current OS. Yours Sincerely, Jianhong Ou TEL: 508-856-5379 LRB 608 Bioinformatician of Bioinformatics core at Department of Molecular, Cell and Cancer Biology 364 Plantation Street

Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

Dear Herve, After reinstalling BiocGenerics, there is no errors any more. Thank you very much. Yours Sincerely, Jianhong Ou TEL: 508-856-5379 LRB 608 Bioinformatician of Bioinformatics core at Department of Molecular, Cell and Cancer Biology 364 Plantation Street Worcester, MA 01605 On

[Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

Hi, I got error when I update S4Vectors in R 3.3 RC r70564 today. I also tried r70549, same error like this > biocLite() BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.21.6), R 3.3.0 RC (2016-04-28 r70564). Old packages: 'S4Vectors' Update all/some/none? [a/s/n]:

Re: [Bioc-devel] could not install S4Vectors in Mac OS 10.8.5

This question should probably go on the support site as it is not about package development. You should update to Mavericks or higher. Earlier versions of Mac OS X are no longer officially supported by R or Bioconductor (that's why a binary is not available). Dan - Original Message

[Bioc-devel] select(Homo.sapiens,...) failing

biocValid() says all is well ... > select(Homo.sapiens, keys="1001", keytype="ENTREZID", columns="SYMBOL") *Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : * * object '.testSelectArgs' not found* > sessionInfo() R version 3.3.0 beta (2016-04-01 r70412) Platform:

Re: [Bioc-devel] some new warnings in a package

> So yes, you should update the NAMESPACE file following the warning > message you see in your build report. Hi Martin, I did not encounter such a note on importing from base packages ever before - but ok, I followed your suggestion and added the imports. However all remaining NOTEs and WARNINGs

Re: [Bioc-devel] some new warnings in a package

On 05/02/2016 11:11 AM, Ludwig Geistlinger wrote: I encounter the same issue with EnrichmentBrowser - and apparently, several other packages too, e.g. ensembldb, erma, ExiMiR ... The warnings seem to be, at first glance, linked to messages e.g. for masking:

Re: [Bioc-devel] some new warnings in a package

I encounter the same issue with EnrichmentBrowser - and apparently, several other packages too, e.g. ensembldb, erma, ExiMiR ... The warnings seem to be, at first glance, linked to messages e.g. for masking: --- * checking S3

Re: [Bioc-devel] Update of data packages in RTCGA Family/Factory of R Packages

Thanks a lot! So I'll contact you after mid-May :) [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Making transcriptLength function a method in GenomicFeatures?

Hi Herve, passing down additional arguments to the internal exonsBy, cdsBy, fiveUTRsByTranscript and threeUTRsByTranscript would do it! That would be great, thanks. cheers, jo > On 02 May 2016, at 07:38, Hervé Pagès wrote: > > Hi Johannes, > > We can make