Thanks for the speedy response Sean. I'll switch back to the version using a file name shortly.
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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
