seandavi
commented
3 years ago It looks like the downloaded file from NCBI might have been incomplete or corrupted. Restarting the R session (to clear the GEOquery cache) and trying again might result in success. I was able to process this particular accession without problems using the same version of GEOquery (2.61.1) without any problems. I'm going to go ahead and close this, but if you continue to have problems after trying a new R session and re-running, feel free to reopen.
HELLO! I am trying to run an R Script! When I am trying to run this command: " gse <- getGEO("GSE181063", GSEMatrix = TRUE)" every single time I get that error: Found 1 file(s) GSE181063_series_matrix.txt.gz Error in data.table::fread(fname, sep = "") : File '/var/folders/_0/7mxf7f790995tf1k4gb52sj00000gn/T//Rtmp3Ay0BD/GSE181063_series_matrix.txt.gz' does not exist or is non-readable.
R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.6
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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 base
other attached packages: [1] dplyr_1.0.7 GEOquery_2.61.1 Biobase_2.52.0 BiocGenerics_0.38.0
loaded via a namespace (and not attached): [1] xml2_1.3.2 magrittr_2.0.1 hms_1.1.1 tidyselect_1.1.1 R6_2.5.1 rlang_0.4.12
[7] fansi_0.5.0 tools_4.1.1 data.table_1.14.2 utf8_1.2.2 ellipsis_0.3.2 remotes_2.4.1
[13] tibble_3.1.5 lifecycle_1.0.1 crayon_1.4.1 tidyr_1.1.4 BiocManager_1.30.16 purrr_0.3.4
[19] readr_2.0.2 tzdb_0.1.2 vctrs_0.3.8 curl_4.3.2 glue_1.4.2 limma_3.48.3
[25] compiler_4.1.1 pillar_1.6.4 generics_0.1.0 pkgconfig_2.0.3
thanks