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