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Enter the body of text here Hi I am unable to extract supplementary files from GSE146963 dataset using GEOquery package. Kindly help.
getGEOSuppFiles("GSE146963")
Error message:
Error in getGEOSuppFiles("GSE146963") :
Failed to download C:/Users/durga/OneDrive/BIOINFORMATICS/OVARIAN_META_ANALYSIS/ARRAY_EXPRESS/GSE146963/OLIGO_GSE146963/GSE146963/GSE146963_RAW.tar!
In addition: Warning message:
In file.remove(destfile) :
cannot remove file 'C:/Users/durga/OneDrive/BIOINFORMATICS/OVARIAN_META_ANALYSIS/ARRAY_EXPRESS/GSE146963/OLIGO_GSE146963/GSE146963/GSE146963_RAW.tar', reason 'Permission denied'
sessionInfo( )
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] GEOquery_2.64.2 oligo_1.60.0 Biostrings_2.64.0 GenomeInfoDb_1.32.3 XVector_0.36.0 IRanges_2.30.0 S4Vectors_0.34.0
[8] Biobase_2.56.0 oligoClasses_1.58.0 BiocGenerics_0.42.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 lattice_0.20-45 tidyr_1.2.0 assertthat_0.2.1 foreach_1.5.2
[6] utf8_1.2.2 R6_2.5.1 RSQLite_2.2.15 pillar_1.8.0 zlibbioc_1.42.0
[11] rlang_1.0.4 curl_4.3.2 rstudioapi_0.13 data.table_1.14.2 blob_1.2.3
[16] Matrix_1.4-1 preprocessCore_1.58.0 splines_4.2.0 readr_2.1.2 RCurl_1.98-1.8
[21] bit_4.0.4 DelayedArray_0.22.0 compiler_4.2.0 pkgconfig_2.0.3 tidyselect_1.1.2
[26] SummarizedExperiment_1.26.1 tibble_3.1.8 GenomeInfoDbData_1.2.8 ff_4.0.7 codetools_0.2-18
[31] matrixStats_0.62.0 fansi_1.0.3 crayon_1.5.1 dplyr_1.0.9 tzdb_0.3.0
[36] bitops_1.0-7 grid_4.2.0 lifecycle_1.0.1 DBI_1.1.3 magrittr_2.0.3
[41] cli_3.3.0 cachem_1.0.6 affyio_1.66.0 limma_3.52.2 xml2_1.3.3
[46] ellipsis_0.3.2 generics_0.1.3 vctrs_0.4.1 iterators_1.0.14 tools_4.2.0
[51] bit64_4.0.5 glue_1.6.2 purrr_0.3.4 hms_1.1.1 MatrixGenerics_1.8.1
[56] fastmap_1.1.0 BiocManager_1.30.18 GenomicRanges_1.48.0 memoise_2.0.1 affxparser_1.68.1
I'm not able to reproduce this. Are you sure you have permissions on where you are downloading/writing?