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
