Re: [Bioc-devel] Build failing for MutationalPatterns

On 11/30/2017 10:01 AM, Janssen-10, R.R.E. wrote: Dear Martin, Martin writes: On 11/29/2017 11:14 AM, Janssen-10, R.R.E. wrote: Hi Martin, Thanks for your reply! Martin Morgan writes: On 11/29/2017 09:58 AM, Janssen-10, R.R.E. wrote: Dear Bioconductor, The build for MutationalPatterns

Re: [Bioc-devel] Data package timeouts

Thanks Sean! I was seeing timeouts also in recount related to GEOquery which I just recently looked into. On Thu, Nov 30, 2017 at 11:14 AM, Sean Davis wrote: > > On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith wrote: > > > Thanks for the speedy response

Re: [Bioc-devel] Data package timeouts

Hi Mike, I was experiencing similar problems with the BeadArrayUseCases vignette, where using getGEO() from GEOquery was getting stuck in a (seemingly) infinite loop processing a GSE series matrix file. It looks like both of your examples try to do this too, so I suspect it's a similar issue. I

Re: [Bioc-devel] Data package timeouts

Thanks for the report, Mike. The problem was (specifically) in parsing a GSEMatrix file using a filename. This should be fixed in versions 2.46.10 (release) and 2.47.12 (devel). Sean On Thu, Nov 30, 2017 at 4:09 AM, Mike Smith wrote: > Hi Mike, > > I was experiencing

[Bioc-devel] a possible bug in development version of GenomicAlignments

Hi, is this a bug in the development version of GenomicAlignments or compressedList? Or I missed anything? Here is how to repeat the error: > library(GenomicAlignments) > gal1 <- GAlignments( + seqnames=Rle(factor(c("chr1", "chr2", "chr1", "chr3")), + c(1, 3, 2, 4)), +

Re: [Bioc-devel] Build failing for MutationalPatterns

Dear Martin, Martin writes: > On 11/29/2017 11:14 AM, Janssen-10, R.R.E. wrote: >> Hi Martin, >> >> Thanks for your reply! >> >> Martin Morgan writes: >> >>> On 11/29/2017 09:58 AM, Janssen-10, R.R.E. wrote: Dear Bioconductor, The build for MutationalPatterns has been failing for

Re: [Bioc-devel] Data package timeouts

On 11/30/2017 06:05 AM, Mike Smith wrote: Thanks for the speedy response Sean. I'll switch back to the version using a file name shortly. Is there a use case for BiocFileCache in here -- check if the file is in the cache bfcquery(), if so, check whether it needs updating bfcneedsupdate()

Re: [Bioc-devel] Data package timeouts

On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith wrote: > Thanks for the speedy response Sean. I'll switch back to the version > using a file name shortly. > No problem. Let me know if it does not work as expected. Sean > > Cheers, > Mike > > On 30 November 2017 at 11:20,

Re: [Bioc-devel] Build failing for MutationalPatterns

On Thu, Nov 30, 2017 at 10:01 AM, Janssen-10, R.R.E. < r.r.e.janssen...@umcutrecht.nl> wrote: > Dear Martin, > > Martin writes: > > > On 11/29/2017 11:14 AM, Janssen-10, R.R.E. wrote: > >> Hi Martin, > >> > >> Thanks for your reply! > >> > >> Martin Morgan writes: > >> > >>> On 11/29/2017 09:58