Hello, I am currently encountering an error when trying to use the keggList function from KEGGREST in Windows. I am trying to retrieve pathways from the arabidopsis database but am encountering the following error (see code). I have re-installed KEGGREST and this function still isn't working. Googling the issue suggested that the error could be due to the KEGG API moving from http to https. If so I do not know how to change the getUrl function to reflect this. Any help would be greatly appreciated.
keggList("pathway","ath")
Error in curl::curl_fetch_memory(url, handle = handle): Failure when receiving data from the peer
Traceback:
1. keggList("pathway", "ath")
2. .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
3. GET(url)
4. request_perform(req, hu$handle$handle)
5. request_fetch(req$output, req$url, handle)
6. request_fetch.write_memory(req$output, req$url, handle)
7. curl::curl_fetch_memory(url, handle = handle)
###
sessionInfo( )
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] KEGGREST_1.32.0
loaded via a namespace (and not attached):
[1] pillar_1.7.0 compiler_4.1.0 GenomeInfoDb_1.28.4
[4] XVector_0.32.0 base64enc_0.1-3 bitops_1.0-7
[7] tools_4.1.0 zlibbioc_1.38.0 digest_0.6.29
[10] uuid_1.0-3 jsonlite_1.7.3 evaluate_0.14
[13] lifecycle_1.0.1 png_0.1-7 rlang_1.0.1
[16] IRdisplay_1.1 cli_3.2.0 IRkernel_1.3.0.9000
[19] curl_4.3.2 parallel_4.1.0 fastmap_1.1.0
[22] GenomeInfoDbData_1.2.6 repr_1.1.4 httr_1.4.2
[25] Biostrings_2.60.2 vctrs_0.3.8 S4Vectors_0.30.2
[28] IRanges_2.26.0 stats4_4.1.0 glue_1.6.0
[31] R6_2.5.1 fansi_1.0.0 pbdZMQ_0.3-6
[34] ellipsis_0.3.2 htmltools_0.5.2 BiocGenerics_0.38.0
[37] utf8_1.2.2 RCurl_1.98-1.6 crayon_1.5.0
Hi! I was using Bioconductor 3.14 but now that I have updated it as you suggested (and R as well) everything is working fine now. Thanks a lot!