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
