[Bioc-devel] Data package timeouts
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 <michaelisaiahlove at 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
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