I'm getting an error from Annotation::select() from a single specific UniProt accession. Other accesions passed to the code do not cause error. Copying and pasting the accession key to uniprot.org search works fine. Accession is a valid key. Oddly, I've been running this code many time over the last weeks and have not seen this error until today. Simplified code and stack trace follow.
PIG<-org.Ss.eg.db
input_keys="A0A287BB68"
validated="UNIPROT"
output_fields="UNIPROT"
AnnotationDbi::select(PIG, keys=input_keys, keytype=validated, columns=output_fields)
Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for 'UNIPROT'. Please use the keys method to see a listing of valid arguments.
8.
stop(msg)
7.
.testForValidKeys(x, keys, keytype, fks)
6.
testSelectArgs(x, keys = keys, cols = cols, keytype = keytype,
fks = fks, skipValidKeysTest = skipValidKeysTest)
5.
.select(x, keys, columns, keytype, jointype = jointype, ...)
4.
AnnotationDbi::select(db, keys = input_keys, keytype = validated,
columns = output_fields)
3.
AnnotationDbi::select(db, keys = input_keys, keytype = validated,
columns = output_fields)
2.
withCallingHandlers(expr, message = function(c) if (inherits(c,
classes)) tryInvokeRestart("muffleMessage"))
1.
suppressMessages(out_tbl <- AnnotationDbi::select(db, keys = input_keys,
keytype = validated, columns = output_fields))
sessionInfo( )
R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
Matrix products: default
LAPACK version 3.12.1
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
time zone: America/Los_Angeles
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] UniProt.ws_2.48.0 org.Hs.eg.db_3.21.0 org.Ss.eg.db_3.21.0 AnnotationDbi_1.70.0 IRanges_2.42.0
[6] S4Vectors_0.46.0 Biobase_2.68.0 BiocGenerics_0.54.0 generics_0.1.4 elasticnet_1.3
[11] lars_1.3 edgeR_4.6.3 limma_3.64.3 BiocManager_1.30.26 caret_7.0-1
[16] lattice_0.22-7 sparseLDA_0.1-9 ggrepel_0.9.6 MASS_7.3-65 scales_1.4.0
[21] stringi_1.8.7 openxlsx_4.2.8 readxl_1.4.5 lubridate_1.9.4 forcats_1.0.0
[26] stringr_1.5.1 dplyr_1.1.4 purrr_1.1.0 readr_2.1.5 tidyr_1.3.1
[31] tibble_3.3.0 ggplot2_3.5.2 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] DBI_1.2.3 pROC_1.19.0.1 httr2_1.2.1 AnVILBase_1.2.0 rlang_1.1.6
[6] magrittr_2.0.3 compiler_4.5.1 RSQLite_2.4.3 png_0.1-8 vctrs_0.6.5
[11] reshape2_1.4.4 pkgconfig_2.0.3 crayon_1.5.3 fastmap_1.2.0 dbplyr_2.5.0
[16] XVector_0.48.0 utf8_1.2.6 prodlim_2025.04.28 tzdb_0.5.0 UCSC.utils_1.4.0
[21] bit_4.6.0 cachem_1.1.0 GenomeInfoDb_1.44.2 jsonlite_2.0.0 progress_1.2.3
[26] recipes_1.3.1 blob_1.2.4 prettyunits_1.2.0 parallel_4.5.1 R6_2.6.1
[31] RColorBrewer_1.1-3 parallelly_1.45.1 rpart_4.1.24 cellranger_1.1.0 Rcpp_1.1.0
[36] iterators_1.0.14 future.apply_1.20.0 BiocBaseUtils_1.10.0 Matrix_1.7-3 splines_4.5.1
[41] nnet_7.3-20 timechange_0.3.0 tidyselect_1.2.1 rstudioapi_0.17.1 timeDate_4041.110
[46] codetools_0.2-20 curl_7.0.0 rjsoncons_1.3.2 listenv_0.9.1 plyr_1.8.9
[51] withr_3.0.2 KEGGREST_1.48.1 future_1.67.0 survival_3.8-3 BiocFileCache_2.16.1
[56] zip_2.3.3 Biostrings_2.76.0 filelock_1.0.3 pillar_1.11.0 foreach_1.5.2
[61] hms_1.1.3 globals_0.18.0 class_7.3-23 glue_1.8.0 mda_0.5-5
[66] tools_4.5.1 data.table_1.17.8 ModelMetrics_1.2.2.2 gower_1.0.2 locfit_1.5-9.12
[71] grid_4.5.1 ipred_0.9-15 nlme_3.1-168 GenomeInfoDbData_1.2.14 cli_3.6.5
[76] rappdirs_0.3.3 lava_1.8.1 gtable_0.3.6 digest_0.6.37 farver_2.1.2
[81] memoise_2.0.1 lifecycle_1.0.4 hardhat_1.4.2 httr_1.4.7 statmod_1.5.0
[86] bit64_4.6.0-1