On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith <grimbo...@gmail.com> 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, Sean Davis <seand...@gmail.com> wrote: > >> 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 <grimbo...@gmail.com> wrote: >> >>> 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 >>> think the format of those files has changed recently and it seems to be >>> causing a fair few issues with GEOquery. >>> >>> I temporarily settled a solution by getting querying GEO directly rather >>> than using a local file, but it would be nice to get it back working as >>> intended. >>> >>> Mike >>> >>> On 29 November 2017 at 18:56, Michael Love <michaelisaiahl...@gmail.com> >>> wrote: >>> >>> > I got simultaneous timeout notices for 'airway' and 'parathyroidSE' on >>> > both release and devel machines (release was fine leading up to the >>> > Bioc release). >>> > >>> > Not sure what's the issue, I haven't changed these packages in a >>> > while. I checked these out and these both build fine and in ~30s on my >>> > machine (devel branch). >>> > >>> > Here are the reports for release: >>> > >>> > http://bioconductor.org/checkResults/release/data- >>> > experiment-LATEST/airway/malbec1-buildsrc.html >>> > http://bioconductor.org/checkResults/release/data-experiment-LATEST/ >>> > parathyroidSE/malbec1-buildsrc.html >>> > >>> > The vignettes are here: >>> > >>> > http://bioconductor.org/packages/3.6/data/experiment/ >>> > vignettes/airway/inst/doc/airway.html >>> > http://bioconductor.org/packages/3.6/data/experiment/ >>> > vignettes/parathyroidSE/inst/doc/parathyroidSE.pdf >>> > >>> > best, >>> > Mike >>> > >>> > _______________________________________________ >>> > Bioc-devel@r-project.org mailing list >>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> > >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> >> >> -- >> Sean Davis, MD, PhD >> Center for Cancer Research >> National Cancer Institute >> National Institutes of Health >> Bethesda, MD 20892 >> https://seandavi.github.io/ >> https://twitter.com/seandavis12 >> > > -- Sean Davis, MD, PhD Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda, MD 20892 https://seandavi.github.io/ https://twitter.com/seandavis12 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
