keggList curl::curl_fetch_memory(url, handle = handle) ERROR
1
0
Entering edit mode
@2fc609cf
Last seen 19 months ago
United Kingdom

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          
​
URL KEGGREST • 1.9k views
ADD COMMENT
0
Entering edit mode
shepherl 4.1k
@lshep
Last seen 4 hours ago
United States

What version of Bioconductor are you using? Is it possible to update your version of R and therefore Bioconductor? I see you are using R 4.1 which means 3.13 or 3.14 -- I currently cannot reproduce this using Bioconductor 3.16/3.17 but can using 3.14 so it seems like it was corrected in a more recent version of the package.

ADD COMMENT
0
Entering edit mode

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!

ADD REPLY

Login before adding your answer.

Traffic: 568 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6