Unable to download supplementary files from GSE146963 using GEOquery
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Entering edit mode
Durga ▴ 10
@76477757
Last seen 6 weeks ago
India

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
GEOquery • 148 views
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0
Entering edit mode

I'm not able to reproduce this. Are you sure you have permissions on where you are downloading/writing?

> getGEOSuppFiles("GSE146963")
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE146nnn/GSE146963/suppl//GSE146963_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 1335838720 bytes (1274.0 MB)
downloaded 1274.0 MB

                                                   size isdir mode
F:/pkgbuild/temp/GSE146963/GSE146963_RAW.tar 1335838720 FALSE  666
                                                           mtime
F:/pkgbuild/temp/GSE146963/GSE146963_RAW.tar 2022-08-18 10:02:09
                                                           ctime
F:/pkgbuild/temp/GSE146963/GSE146963_RAW.tar 2022-08-18 10:02:06
                                                           atime exe
F:/pkgbuild/temp/GSE146963/GSE146963_RAW.tar 2022-08-18 10:02:09  no
> sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 20348)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] GEOquery_2.64.2     Biobase_2.56.0      BiocGenerics_0.42.0

loaded via a namespace (and not attached):
 [1] xml2_1.3.3        magrittr_2.0.3    hms_1.1.1         tidyselect_1.1.2
 [5] R6_2.5.1          rlang_1.0.4       fansi_1.0.3       dplyr_1.0.9
 [9] data.table_1.14.2 utf8_1.2.2        cli_3.3.0         DBI_1.1.3
[13] ellipsis_0.3.2    assertthat_0.2.1  tibble_3.1.8      lifecycle_1.0.1
[17] purrr_0.3.4       readr_2.1.2       tzdb_0.3.0        tidyr_1.2.0
[21] vctrs_0.4.1       curl_4.3.2        glue_1.6.2        limma_3.52.2
[25] compiler_4.2.1    pillar_1.8.0      generics_0.1.3    pkgconfig_2.0.3
>
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2
Entering edit mode
@james-w-macdonald-5106
Last seen 40 minutes ago
United States

The error indicates that R doesn't have permissions to remove a file from that directory, which may imply that it doesn't have permissions to write either. Maybe try a different (non-OneDrive) directory.

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