org.Hs.eg.db issue
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k.panov • 0
@kpanov-15226
Last seen 29 days ago
United Kingdom

Hi, I encounter a strange issue with org.Hs.eg.db: Execution of this code:

"select(org.Hs.eg.db, keys="1956", columns="SYMBOL", keytype="ENTREZID")" returns:
 'select()' returned 1:1 mapping between keys and columns
  ENTREZID SYMBOL
1     1956   EGFR

as expected, but execution of this:

"select(org.Hs.eg.db,keys="EGFR", columns=c("ENTREZID", "GENENAME"), keytype="SYMBOL")"; returns: Error: unable to open database file.

I removed/installed org.Hs.eg.db several times using different approaches (e.g. with/without dependencies, even installed next version of R (4.4.2), but no luck. All checks that were recommended by ChatGPT passed OK. Any ideas?

sessionInfo()
R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.utf8  LC_CTYPE=English_United Kingdom.utf8    LC_MONETARY=English_United Kingdom.utf8
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.utf8    
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] org.Hs.eg.db_3.20.0  AnnotationDbi_1.68.0 IRanges_2.40.1       S4Vectors_0.44.0     Biobase_2.66.0       BiocGenerics_0.52.0 
loaded via a namespace (and not attached):
 [1] crayon_1.5.3            vctrs_0.6.5             httr_1.4.7              cli_3.6.3               rlang_1.1.4             DBI_1.2.3              
 [7] png_0.1-8               UCSC.utils_1.2.0        jsonlite_1.8.9          bit_4.5.0.1             Biostrings_2.74.1       KEGGREST_1.46.0        
[13] fastmap_1.2.0           GenomeInfoDb_1.42.1     memoise_2.0.1           BiocManager_1.30.25     compiler_4.4.2          RSQLite_2.3.9          
[19] blob_1.2.4              pkgconfig_2.0.3         XVector_0.46.0          rstudioapi_0.17.1       R6_2.5.1                GenomeInfoDbData_1.2.13
[25] tools_4.4.2             bit64_4.5.2             zlibbioc_1.52.0         cachem_1.1.0
org.Hs.eg.db • 179 views
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installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(

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