Re: [Bioc-devel] Bioconductor and R 3.3.3: Error in c(x, values) : could not find symbol "recursive" in environment of the generic function

Thanks Hervé and Henrik, I have also been experiencing the same issues. I innocently typed "sudo apt-get upgrade" in Ubuntu and this broke my Bioconductor install. Regards, Jason -Original Message- From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of Henrik

[R-pkg-devel] Extending an S3 method, but putting the package in Suggests?

Hi, Cross-posted from SO: http://stackoverflow.com/questions/42776058/extending-an-s3-generic-from-an-optional-package I have a package which provides an as.FlexTable method for its objects, extending the S3 generic from the ReporteRs package. So, my NAMESPACE file, generated by roxygen, has

[Bioc-devel] devel builds: oaxaca phase out

oaxaca has been removed from the build report and toluca2 is now the official Mac devel builder. Herve has applied all system updates to toluca2 and is smoothing out the final kinks. Lori is finalizing the transition of the Single Package Builder from oaxaca to toluca2 and once that's done oaxaca

[Rd] simplify2array(higher=TRUE, listOfSingleRowDataframes)

I noticed that simplify2array acted oddly when given a list of data.frames of various sizes. If the data.frames have one row, it makes a new first dimension with the dimname equal to rownames(firstDataframe). That dimension does not appear for data.frames with other numbers of rows. >

[R-pkg-devel] Creating a new package dependent on Igraph

Hello all, We have created a new package called dgraph which contains all the igraph codebase along with our graph decomposition functions. We have overwritten the Namespace and exported only our functions.So, the user will not be able to access the functions of igraph through our package dgraph.

Re: [Rd] strptime("1","%m") returns NA

Hi Martyn, Thanks for finding that stuff in the documentation, and apologies for not reading the whole thing carefully. I guess when I got to the minutiae about printing years before '999', I started to skim. My vote is for more sensible / standard behavior, but I guess this has probably been

Re: [Rd] named arguments in formula and terms

Martin, thanks for the follow-up! On Mon, 13 Mar 2017, Martin Maechler wrote: Dear Achim, Achim Zeileis on Fri, 10 Mar 2017 15:02:38 +0100 writes: > Hi, we came across the following unexpected (for us) > behavior in terms.formula: When determining

Re: [Bioc-devel] Chromosome order in GRangesForUCSCGenome

Looks like UCSC has started sorting the chromosomes by size. I made 1.35.9 use sortSeqlevels() to normalize the order of them. On Mon, Mar 13, 2017 at 3:05 AM, Bernat Gel wrote: > I'm downloading genome information from UCSC using the > GRangesForUCSCGenome from rtracklayer and

Re: [Bioc-devel] question on package build

I can investigate this and see what was going on however, you deleted the first comment when submitting packages that included the link to your github repository. Until you add the section agreeing to the Bioconductor terms of package review and include the link to your github repository we

[Bioc-devel] question on package build

Hi I have develop a Bioconductor package and submit the issue to build and check. It has passed the build and check on Windows and Mac OS. But I don't know why build takes less than 1 minute on Windows and Mac OS but more than 10 minutes on your Linux machine? The report of build and

[Bioc-devel] Chromosome order in GRangesForUCSCGenome

I'm downloading genome information from UCSC using the GRangesForUCSCGenome from rtracklayer and it seems that the chromosome order is incorrect (or at least non-canonical). > seqlevels(GRangesForUCSCGenome(genome="hg19")) [1] "chr1" "chr2" "chr3" "chr4"

Re: [Rd] named arguments in formula and terms

Dear Achim, > Achim Zeileis > on Fri, 10 Mar 2017 15:02:38 +0100 writes: > Hi, we came across the following unexpected (for us) > behavior in terms.formula: When determining whether a term > is duplicated, only the order of the arguments in