enrichWP error

[LoetC]

Hi,

When running the "enrichWP" function with Entrez gene IDs as input I get the following error:

No gene can be mapped.... -->
Expected input gene ID: -->
return NULL...

while in other 'enrich' functions (enrichKEGG, enrichGO, ...) it works. Also, when running get_wp_organisms() function to identify the organisms, it only returns 3 organisms ("Caenorhabditis elegans", "Bos taurus", "Arabidopsis thaliana" ) which may explain why they cannot be mapped using my organism ("Homo sapiens").

I have tried reinstalling clusterProfiler and running in a new session without any other packages to overcome conflicting functions, but no success so far. Any ideas on how to resolve?

Session info:
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.4.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Amsterdam
tzcode source: internal

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

other attached packages:
[1] clusterProfiler_4.10.1

loaded via a namespace (and not attached):
[1] DBI_1.2.3 bitops_1.0-8 gson_0.1.0 shadowtext_0.1.4 gridExtra_2.3
[6] rlang_1.1.4 magrittr_2.0.3 DOSE_3.28.2 compiler_4.3.1 RSQLite_2.3.7
[11] png_0.1-8 vctrs_0.6.5 reshape2_1.4.4 stringr_1.5.1 pkgconfig_2.0.3
[16] crayon_1.5.3 fastmap_1.2.0 XVector_0.42.0 ggraph_2.2.1 utf8_1.2.4
[21] HDO.db_0.99.1 enrichplot_1.22.0 purrr_1.0.2 bit_4.0.5 zlibbioc_1.48.2
[26] cachem_1.1.0 aplot_0.2.3 GenomeInfoDb_1.38.8 jsonlite_1.8.8 blob_1.2.4
[31] BiocParallel_1.36.0 tweenr_2.0.3 parallel_4.3.1 R6_2.5.1 stringi_1.8.4
[36] RColorBrewer_1.1-3 GOSemSim_2.28.1 Rcpp_1.0.13 IRanges_2.36.0 Matrix_1.6-5
[41] splines_4.3.1 igraph_2.0.3 tidyselect_1.2.1 qvalue_2.34.0 rstudioapi_0.16.0
[46] viridis_0.6.5 codetools_0.2-20 lattice_0.22-6 tibble_3.2.1 plyr_1.8.9
[51] Biobase_2.62.0 treeio_1.29.1 withr_3.0.1 KEGGREST_1.42.0 gridGraphics_0.5-1
[56] scatterpie_0.2.4 polyclip_1.10-7 Biostrings_2.70.3 pillar_1.9.0 ggtree_3.10.1
[61] stats4_4.3.1 ggfun_0.1.6 generics_0.1.3 RCurl_1.98-1.16 S4Vectors_0.40.2
[66] ggplot2_3.5.1 munsell_0.5.1 scales_1.3.0 tidytree_0.4.6 glue_1.7.0
[71] lazyeval_0.2.2 tools_4.3.1 data.table_1.16.0 fgsea_1.28.0 fs_1.6.4
[76] graphlayouts_1.1.1 fastmatch_1.1-4 tidygraph_1.3.1 cowplot_1.1.3 grid_4.3.1
[81] tidyr_1.3.1 ape_5.8 AnnotationDbi_1.64.1 colorspace_2.1-1 nlme_3.1-166
[86] GenomeInfoDbData_1.2.11 patchwork_1.3.0 ggforce_0.4.2 cli_3.6.3 fansi_1.0.6
[91] viridisLite_0.4.2 dplyr_1.1.4 gtable_0.3.5 yulab.utils_0.1.7 digest_0.6.37
[96] BiocGenerics_0.48.1 ggrepel_0.9.6 ggplotify_0.1.2 farver_2.1.2 memoise_2.0.1
[101] lifecycle_1.0.4 httr_1.4.7 GO.db_3.18.0 bit64_4.0.5 MASS_7.3-60

[guidohooiveld]

Please show the lines of code you used as well as some of the input ids.

Also, you may first want to update to the the latest versions of R and Bioconductor (your's is > 1 year old). I am suggesting this because under the hood clusterProfiler downloads files from the internet (e.g. KEGG, WiKiPathways), and access/locations to some of the relevant files has been changed on the server side. This has been fixed but possibly not in your version of clusterProfiler.

See e.g. #559