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I'm attempting to query UniProt with the UniProt.ws package. I ran the same code two days ago with no issues and it ran in maybe a second, but yesterday and today it's kept going indefinitely. I've let it run for at least 17 minutes with the same update message appearing every three seconds. I've updated R, Rstudio, and Bioconductor; all the packages in them; and UniProt.ws itself.
In this example, I've switched out the actual taxID and uniref90 numbers for those referencing all herpesviridae but the issue is the same if I switch taxID numbers and UniRef90 numbers.
library(UniProt.ws)
up <- UniProt.ws(taxId = 548681)
cluster_ids <- c("UniRef90_A0A2P5FU56", "UniRef90_A0A0P8D9T9")
# get protein associated with each uniref90 id
keys <- cluster_ids
columns <- c("gene_names", "sequence")
ktype <- "UniRef90"
ebv_genes <- UniProt.ws::select(up, keys, columns, ktype)
(\) waiting for query completion.......... 00:00:02
(-) waiting for query completion.......... 00:00:05
(/) waiting for query completion.......... 00:00:08
sessionInfo():
sessionInfo()
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices datasets utils methods base
other attached packages:
[1] ggbiplot_0.6.2 factoextra_1.0.7 ggfortify_0.4.17 ggbreak_0.1.4 ggrepel_0.9.6
[6] pheatmap_1.0.12 nlme_3.1-167 respR_2.3.3 pwalign_1.2.0 msa_1.38.0
[11] Biostrings_2.74.1 GenomeInfoDb_1.42.3 XVector_0.46.0 IRanges_2.40.1 S4Vectors_0.44.0
[16] janitor_2.2.1 stringi_1.8.4 magrittr_2.0.3 lubridate_1.9.4 forcats_1.0.0
[21] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.4 readr_2.1.5 tidyr_1.3.1
[26] tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0 UniProt.ws_2.46.1 RSQLite_2.3.9
[31] BiocGenerics_0.52.0 arrow_18.1.0.1 BiocManager_1.30.25
loaded via a namespace (and not attached):
[1] DBI_1.2.3 httpcache_1.2.0 gridExtra_2.3 rlang_1.1.5
[5] snakecase_0.11.1 compiler_4.4.1 marelac_2.1.11 png_0.1-8
[9] vctrs_0.6.5 pkgconfig_2.0.3 shape_1.4.6.1 crayon_1.5.3
[13] fastmap_1.2.0 dbplyr_2.5.0 rmarkdown_2.29 tzdb_0.4.0
[17] UCSC.utils_1.2.0 oce_1.8-3 gsw_1.2-0 bit_4.5.0.1
[21] xfun_0.50 zlibbioc_1.52.0 cachem_1.1.0 aplot_0.2.4
[25] jsonlite_1.8.9 roll_1.1.7 progress_1.2.3 blob_1.2.4
[29] parallel_4.4.1 prettyunits_1.2.0 R6_2.6.0 RColorBrewer_1.1-3
[33] Rcpp_1.0.14 assertthat_0.2.1 knitr_1.49 seacarb_3.3.3
[37] BiocBaseUtils_1.8.0 timechange_0.3.0 tidyselect_1.2.1 rstudioapi_0.17.1
[41] yaml_2.3.10 curl_6.2.0 rjsoncons_1.3.1 lattice_0.22-6
[45] Biobase_2.66.0 withr_3.0.2 KEGGREST_1.46.0 evaluate_1.0.3
[49] gridGraphics_0.5-1 RcppParallel_5.1.10 BiocFileCache_2.14.0 xml2_1.3.6
[53] pillar_1.10.1 filelock_1.0.3 rsconnect_1.3.4 renv_1.1.1
[57] ggfun_0.1.8 generics_0.1.3 vroom_1.6.5 hms_1.1.3
[61] munsell_0.5.1 scales_1.3.0 glue_1.8.0 tools_4.4.1
[65] data.table_1.16.4 fs_1.6.5 grid_4.4.1 AnnotationDbi_1.68.0
[69] colorspace_2.1-1 patchwork_1.3.0 GenomeInfoDbData_1.2.13 cli_3.6.4
[73] SolveSAPHE_2.1.0 gtable_0.3.6 yulab.utils_0.2.0 digest_0.6.37
[77] ggplotify_0.1.2 farver_2.1.2 memoise_2.0.1 htmltools_0.5.8.1
[81] lifecycle_1.0.4 httr_1.4.7 bit64_4.6.0-1
