[Bioc-devel] Data package timeouts

[Leonardo Collado Torres]

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 <seandavi at gmail.com> wrote:

>
> On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith <grimbough at 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 <seandavi at 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 <grimbough at 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 <
> 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
> >>> >
> >>> > _______________________________________________
> >>> > Bioc-devel at r-project.org mailing list
> >>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>> >
> >>>
> >>>         [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> Bioc-devel at 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]]
>
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> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>

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