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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
