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.

Code should be placed in three backticks as shown below

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

Yes. It told you there was a problem and then it said how to fix it. Did you try that?

Here is a detailed answer to what is going on.

Historical context: GEOquery used readr::read_table() for many years. At some point, read_table() started to use functionality in the vroom package. When vroom limited buffer size, GEOquery started seeing parsing failures that required setting the environment variable VROOM_CONNECTION_SIZE. I could have just set the environment to an arbitrarily large number and left things at that, but changing environment variables in package code is not something any of us should be comfortable doing unless we "own" the environment variable. Addressing the error requires the user to 1) read and understand the error message and 2) iteratively try settings until things work.

So, I refactored GEOquery and replaced readr::read_table() and associated readr functionality with data.table::fread() code; this fixes the error and also benefits from some additional speed from data.table. So, the recommended solution to the error in the original post is to upgrade R to 4.1 or later and reinstall GEOquery to get the matching Bioconductor and GEOquery versions.