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@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 > > _______________________________________________ > 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