Error in .getUrl(url, .flatFileParser) : Not Found (HTTP 404).

[xiefumin1]

im using this package to make kegg ，

> ppp_info <- lapply(lipid_pathway, keggGet)
Error in .getUrl(url, .flatFileParser) : Not Found (HTTP 404).

and fix it with

detach(package:KEGGREST, unload = T)
library(devtools)
devtools::install_github("https://github.com/kozo2/KEGGREST/tree/patch-1")

but it can not work

[lshep]

What is your sessionInfo() to provide your OS/R version and Bioc version. When you say the tried github patch does not work do you receive the same error? Can you run the examples in ?keggGet() and still get the ERROR. If yes after the ERROR is called please also provide a traceback() ; if no can you provide part of lipid_pathway so we can try to replicate?

[xiefumin1]

win11and R4.3.

res <- keggGet(c("cpd:C01290", "gl:G00092")),
##When I run the example, there are no errors generated. 
lipid_pathway <- c("path:ppp00061", "path:ppp00062", "path:ppp00071", "path:ppp00073", "path:ppp00100", "path:ppp00120", "path:ppp00121", "path:ppp00140", "path:ppp00561", "path:ppp00564", "path:ppp00565", "path:ppp00600", "path:ppp00590", "path:ppp00591", "path:ppp00592", "path:ppp01040")
thank you very much

[lshep]

can you provide your sessionInfo() as well please

[xiefumin1]

> sessionInfo()
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8  LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
[1] png_0.1-8         stringr_1.5.0     KEGGREST_1.36.0   R.utils_2.12.2    R.oo_1.25.0      
[6] R.methodsS3_1.8.2

loaded via a namespace (and not attached):
 [1] crayon_1.5.2            httr_1.4.6              cli_3.6.1              
 [4] knitr_1.43              rlang_1.1.1             xfun_0.39              
 [7] highr_0.10              stringi_1.7.12          glue_1.6.2             
[10] S4Vectors_0.38.1        RCurl_1.98-1.12         Biostrings_2.68.1      
[13] stats4_4.3.0            evaluate_0.21           bitops_1.0-7           
[16] IRanges_2.34.0          lifecycle_1.0.3         GenomeInfoDb_1.36.0    
[19] compiler_4.3.0          XVector_0.40.0          rstudioapi_0.14        
[22] R6_2.5.1                curl_5.0.0              GenomeInfoDbData_1.2.10
[25] magrittr_2.0.3          tools_4.3.0             zlibbioc_1.46.0        
[28] BiocGenerics_0.46.0  

[xiefumin1]

lipid_pathway <- c("path:ppp00120", "path:ppp00121", "path:ppp00140") When I use these three paths, this software will report an error.When I delete these three paths, the package can function normally.

[lshep]

I think this is accurate -- If you check the urls something like ppp00061 works https://rest.kegg.jp/get/path:ppp00061 while ppp00120 does not https://rest.kegg.jp/get/path:ppp00120

[xiefumin1]

yes, ppp00061 works, but ppp00120 does not. It looks like there's a problem with the KEGG server.