Re: [Bioc-devel] read SBML file from BiGG database, unit consistency check

2013-08-07 Thread hettling
I contacted the BiGG maintainers and it turns out that the units they have in the SBML document are technically correct for the reconstruction databases, although the validator complains. Since we don't need the units in our package, I found a workaround by just parsing them out: file -

Re: [Bioc-devel] Package Build RSS feeds now available

2013-08-07 Thread Kasper Daniel Hansen
This is awesome, thanks a lot. On Wed, Aug 7, 2013 at 3:44 AM, Laurent Gatto lg...@cam.ac.uk wrote: On 7 August 2013 01:20, Dan Tenenbaum dtene...@fhcrc.org wrote: The web page at http://www.bioconductor.org/developers/rss-feeds/ has been updated with instructions for retrieving

Re: [Bioc-devel] Package Build RSS feeds now available

2013-08-07 Thread Henrik Bengtsson
FYI, it appears that packages with periods in their names doesn't work, e.g. http://bioconductor.org/rss/build/packages/aroma.light.rss http://bioconductor.org/rss/build/packages/cn.farms.rss vs http://bioconductor.org/rss/build/packages/illuminaio.rss Thanks, Henrik On Wed, Aug 7, 2013 at

Re: [Bioc-devel] Package Build RSS feeds now available

2013-08-07 Thread Dan Tenenbaum
On Wed, Aug 7, 2013 at 6:44 AM, Henrik Bengtsson h...@biostat.ucsf.edu wrote: FYI, it appears that packages with periods in their names doesn't work, e.g. http://bioconductor.org/rss/build/packages/aroma.light.rss http://bioconductor.org/rss/build/packages/cn.farms.rss vs

Re: [Bioc-devel] R CMD check and par(mfrow=…) in vignettes

2013-08-07 Thread Martin Maechler
Martin Morgan mtmor...@fhcrc.org on Wed, 7 Aug 2013 05:14:35 -0700 writes: On 08/06/2013 05:25 AM, Wolfgang Huber wrote: Hi one of my packages [1] has several places in its vignette where multi-panel figures are generated via the likes of par(mfrow=c(4,2)) within

[Bioc-devel] session info of Single Package Builder Machines

2013-08-07 Thread hettling
Dear all, I try to resubmit my package in the file submit tracker after completing the package revisions. I tested my package on various machines with R 3.0.1 and Bioc 2.13, build and check proceed without any errors or warnings. However, the built with the Single Package Builder fails on the

Re: [Bioc-devel] session info of Single Package Builder Machines

2013-08-07 Thread Hettling, J.
Hi, My sessionInfo() gave the same versions for all packages compared to the ones on zin1. I still do not know why it build without problems on my machines and threw an error on zin. However, since you indicated where things went wrong: So it's a problem in the plot method of the hyperdraw