[Bioc-devel] [GenomicFeatures] no pkgName found. makeTxDbPackage() called after txdb created from GFF3 file

2013-02-06 Thread Tengfei Yin
Dear all, I am trying to build a txdb object from gff3 for soybean data and try to make it a package. Code used like this gmax189 <- makeTranscriptDbFromGFF("~/Gmax_189_gene_exons.gff3", format = "gff3", species = "Glycine max",

[Bioc-devel] small request on graph::graphBAM()

2013-02-06 Thread Robert Castelo
dear maintainers of the graph package, i have a small request for the constructor function graphBAM() from the graph package. the current help page of the graphBAM() constructor says the following about the argument called 'nodes': A character vector of node labels. Use this to add degree z

Re: [Bioc-devel] BioC question

2013-02-06 Thread Thomas Sandmann
Dear Dan, great, problem solved. Thanks a lot ! Thomas [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] BioC question

2013-02-06 Thread Dan Tenenbaum
On Wed, Feb 6, 2013 at 10:04 AM, Thomas Sandmann wrote: > Dear BioC developers, > > I upgraded to R 3.0.0 on my Mac (10.6.8) to make my gCMAP package ready for > the next BioC release. > Afterward, I reinstalled all the required BioC packages using biocLite. > > My package depends on "org.Hs.eg.db

[Bioc-devel] BioC question

2013-02-06 Thread Thomas Sandmann
Dear BioC developers, I upgraded to R 3.0.0 on my Mac (10.6.8) to make my gCMAP package ready for the next BioC release. Afterward, I reinstalled all the required BioC packages using biocLite. My package depends on "org.Hs.eg.db". Unfortunately, installing the latest "org.Hs.eg.db" via biocLite g