[Bioc-devel] GEOquery run into problem with Sys.setenv("VROOM_CONNECTION_SIZE")

[Alexey Sergushichev]

Hi,

This issue was fixed by Sean Davis in 2.63.1 (
https://github.com/seandavi/GEOquery/commit/08ff9c3524) and I believe he
has back-ported it into 2.62.1 as well. So you can install the latest
version and try again.

Best,
Alexey

On Wed, Dec 1, 2021 at 11:06 PM array chip via Bioc-devel <
bioc-devel using r-project.org> wrote:

> Hi, I a using GEOquery to download some microarray datasets. It worked
> previously without any problem under old R version (3.5 probably), but now
> run into problem now I've updated R to version 4.0.5.
>
>
> library(GEOquery)
> gse<-getGEO(GEO="GSE137140")
>
> # Found 1 file(s)
> # GSE137140_series_matrix.txt.gz
> # trying URL '
> https://ftp.ncbi.nlm.nih.gov/geo/series/GSE137nnn/GSE137140/matrix/GSE137140_series_matrix.txt.gz
> '
> # Content type 'application/x-gzip' length 45700106 bytes (43.6 MB)
> # downloaded 43.6 MB
>
> # Error: The size of the connection biffer (131072) was not large enough
> # to fit a complete line:
> #    Increase it by setting 'Sys.setenv("VROOM_CONNECTION_SIZE")'
>
> sessionInfo( )
>
> R version 4.0.5 (2021-03-31)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 19042)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United
> States.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] limma_3.46.0        GEOquery_2.58.0
> Biobase_2.50.0      BiocGenerics_0.36.1 BiocManager_1.30.12
>
> loaded via a namespace (and not attached):
> [1] xml2_1.3.3       magrittr_2.0.1
> hms_1.1.1        bit_4.0.4        tidyselect_1.1.1 R6_2.5.1
> rlang_0.4.12     fansi_0.5.0
> [9] dplyr_1.0.7      tools_4.0.5      vroom_1.5.7      utf8_1.2.2
> DBI_1.1.1        withr_2.4.3      ellipsis_0.3.2   bit64_4.0.5
> [17] assertthat_0.2.1 tibble_3.1.6     lifecycle_1.0.1  crayon_1.4.2
> tidyr_1.1.4      purrr_0.3.4      readr_2.1.1      tzdb_0.2.0
> [25] vctrs_0.3.8      curl_4.3.2       glue_1.5.1       compiler_4.0.5
> pillar_1.6.4     generics_0.1.1   pkgconfig_2.0.3
>
>
> I tried to increase the connection buffer by
> Sys.setenv("VROOM_CONNECTION_SIZE"=131072*5), but no success.
>
> Can someone tell me what's going on? Why it worked flawlessly, but now the
> problem with new R and new bioconductor versions?
>
> Thanks,
>
> John
>
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