org.Hs.eg.db issue
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k.panov • 0
@kpanov-15226
Last seen 8 hours 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 • 59 views
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installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(

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