Thanks, Leo. It turns out that that accession is not "public" yet; the "file" that GEOquery gets is just an HTML page saying so.
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1062236 I'll work on fix to catch such problems. Sean On Tue, Dec 5, 2017 at 1:48 PM, Leonardo Collado Torres <lcoll...@jhu.edu> wrote: > 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 > <lcoll...@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 <seand...@gmail.com> wrote: > >> > >> > >> On Thu, Nov 30, 2017 at 6:05 AM, Mike Smith <grimbo...@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 <seand...@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 <grimbo...@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 < > 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 > >> >>> > >> >> > >> >> > >> >> > >> >> -- > >> >> 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]] > >> > >> _______________________________________________ > >> Bioc-devel@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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
