[Bioc-devel] Data package timeouts

Hi Sean,

I'm still seeing some timeouts with GEOquery 2.46.10 on bioc-release.
Here's a quick example:

library('GEOquery')
getGEO('GSM1062236', getGPL = FALSE)

I found it from
https://github.com/leekgroup/recount/blob/master/tests/
testthat/test-misc.R#L19

Best,
Leo

library('GEOquery')

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ?BiocGenerics?

The following objects are masked from ?package:parallel?:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ?package:stats?:

    IQR, mad, sd, var, xtabs

The following objects are masked from ?package:base?:

    anyDuplicated, append, as.data.frame, cbind, colMeans, colnames,
    colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

getGEO('GSM1062236', getGPL = FALSE)

File stored at:
/var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T//RtmpAyQR3U/
GSM1062236.soft
## Force terminate after a long running time
^C

sessionInfo()

R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/
Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/
Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GEOquery_2.46.10    Biobase_2.38.0      BiocGenerics_0.24.0
[4] colorout_1.1-2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14     tidyr_0.7.2      dplyr_0.7.4      assertthat_0.2.0
 [5] R6_2.2.2         magrittr_1.5     rlang_0.1.4      bindrcpp_0.2
 [9] limma_3.34.2     xml2_1.1.1       readr_1.1.1      glue_1.2.0
[13] purrr_0.2.4      hms_0.4.0        compiler_3.4.2   pkgconfig_2.0.1
[17] bindr_0.1        tibble_1.3.4


On Thu, Nov 30, 2017 at 11:56 AM, Leonardo Collado Torres
<lcollado at jhu.edu> wrote:

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

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