Re: [Bioc-devel] Issue with GenomeInfoDb

2017-07-17 Thread Martin Morgan
Thanks Ken the list filters attachements that are not of the following type text/x-diff multipart/mixed multipart/alternative text/plain text/html application/pgp-signature application/postscript application/pdf image/png message/rfc822 application/x-xz application/x-gzip so please feel free to

Re: [Bioc-devel] Issue with GenomeInfoDb

2017-07-17 Thread Weiss, Kenneth
Greetings, Attached is the patch file GenomeInfoDb.patch noted below. Cheers, Ken From: Weiss, Kenneth Sent: Monday, July 17, 2017 11:33 AM To: 'bioc-devel@r-project.org' Cc: Mark Montague (markm...@umich.edu) Subject: Issue with GenomeInfoDb Greetings, I provide support for an HPC cluster at

[Bioc-devel] Issue with GenomeInfoDb

2017-07-17 Thread Weiss, Kenneth
Greetings, I provide support for an HPC cluster at the University of Michigan. Recently we had a user approach us with the following problem: I have an issue about using the following package/function in R. *library("GenomeInfoDb")* *GenomeInfoDb::Seqinfo(genome = "mm10")* The function is

Re: [Bioc-devel] Bioconductor issue 396: Vignette building problem for OPWpaper package

2017-07-17 Thread Wolfgang Huber
Hi Shakil Why don't you use the regular mechanism for data in packages, e.g.: https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Data-in-packages Btw, is the preprint of the associated paper out already? best wishes Wolfgang 17.7.17 10:25, Shakil Mohamad

[Bioc-devel] Bioconductor issue 396: Vignette building problem for OPWpaper package

2017-07-17 Thread Shakil Mohamad
Hi, I manually stored some .RDATA in one of my package's folder named 'results' located in the 'inst' folder ( https://github.com/mshasan/OPWpaper/inst/simulations/results). I need to use those .RDATA to build the vignettes. For example, one of my vignettes' names is 'FWER_and_FDR' in which I

Re: [Bioc-devel] improving navigation within workflows

2017-07-17 Thread Aaron Lun
Hi Andrzej, Interesting. I also didn't realize that we could get figure referencing via bookdown, that's nice to know. I was thinking that the floating TOC could go onto the right margin, but I guess that doesn't fit anymore now that you have the footnotes and figure captions. CRAN-style