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] Data package timeouts
7 messages · Michael Love, Mike Smith, Martin Morgan +2 more
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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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
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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 <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
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On 11/30/2017 06:05 AM, Mike Smith wrote:
Thanks for the speedy response Sean. I'll switch back to the version using a file name shortly.
Is there a use case for BiocFileCache in here -- check if the file is in the cache bfcquery(), if so, check whether it needs updating bfcneedsupdate() and perhaps bfcupdate() ? this might make the overall download process more robust, and would certainly save on build time. Martin
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
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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
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-- 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]]
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
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-- 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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