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

Andrzej, Sorry, I didn't realize that line was coming from my own Makefile. The Makefile was there for historic reasons, but I think can be removed now, so that will probably fix the problem. Kevin On 02/08/2018 02:39 AM, Andrzej Oleś wrote: > Dear Kevin, > > thank you for reporting the

Re: [Bioc-devel] rsvg on mac

Valerie, I'm not sure I understand. I looked at another package that is currently installed on the mac devel machine, DiagrammeR (https://cran.r-project.org/package=DiagrammeR), and it has the same set of links on the CRAN site as rsvg does. In particular, it does not show a r-devel

Re: [Bioc-devel] Issues with GenomicRanges updates

Hi Nathan, You're right, there was a remaining issue. It should be fixed in IRanges 2.13.26. Make sure to also get S4Vectors 0.17.32 (IRanges 2.13.26 requires it). The 2 updated packages should become available via biocLite() in about 24 hours but you can get them now directly from

Re: [Bioc-devel] Help with GWASTools

Hi, Try the following. Just print "bed.fn" to see if they are imported correctly. And use "snpgdsBED2GDS(... verbose=TRUE)" to print more detailed information or error log. Qian Liu Bioconductor Core Team Roswell Park Cancer Institute library(SNPRelate) (bed.fn <- system.file("extdata",

Re: [Bioc-devel] Access to push to pacakges Polyester and Ballgown

Hi Jack, Have you gone through the steps outlined here? https://bioconductor.org/developers/how-to/git/ Specifically, have you added ssh keys? https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform If you have not added keys, you'll need to.

[Bioc-devel] Access to push to pacakges Polyester and Ballgown

Hi Bioc team, I'm currently maintaining the packages Ballgown and polyester. However, I haven't been able to access the new system since the change in system. I'm wondering if I would be able to be give access? I have included the maintainers on file for those packages as well. Best, Jack

Re: [Bioc-devel] warning: checking Rd cross-references

On 02/12/2018 07:01 AM, Claris Baby via Bioc-devel wrote: Dear all,I am trying to build a package for RNA-seq analysis combining different existing packages in bioconductor and am facing problem while trying to run Check PackageThere is no error but a warning saying checking Rd

Re: [Bioc-devel] Issues with GenomicRanges updates

Hi Herve, The updates have indeed solved those issues for that sample -- However, when you try to apply a more complicated function, I am getting the same error. Here's a reproducible example of the error again, this time using the latest GenomicRanges and IRanges packages:

[Bioc-devel] warning: checking Rd cross-references

Dear all,I am trying to build a package for RNA-seq analysis combining different existing packages in bioconductor and am facing problem while trying to run Check PackageThere is no error but a warning saying checking Rd cross-references ... WARNING Missing link or links in documentation object

[Bioc-devel] "Error: duplicate commits" when pushing FamAgg to Bioconductor git

Dear all, I'm unable to push my recent changes to FamAgg to the Bioconductor git repo (see below for the error message). I did try the suggested fix but without any success - seems the duplicated commits are in Bioconductor and not github. thankful for any help or advise The error message is:

Re: [Bioc-devel] Bug in Biostrings::reverse?

I have been able to make it work now, sorry for the previous email. Best, Leandro. On Mon, Feb 12, 2018 at 4:52 AM, Leandro Roser wrote: > > Dear BioC, > > > Using the devel version of Biostrings (2.47.9) i am obtaining an error > message with the 'reverse' function