I was using edgeR for an exact test (output to a variable "et"), done by exactTest() function. Then I used goana(et, species='Hs') function to do GO enrichment analysis and kegga(et, species='Hs') to do KEGG analysis. GO analysis was OK but KEGG analysis went wrong (see the code and output below). I googled but couldn't find useful hints. Anyone have any idea of it? Thanks in advance.
> et <- exactTest(y) > keg <- kegga(et,species='Hs') Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached > traceback() 12: .Call(R_curl_fetch_memory, url, handle) 11: curl::curl_fetch_memory(url, handle = handle) 10: request_fetch.write_memory(req$output, req$url, handle) 9: request_fetch(req$output, req$url, handle) 8: request_perform(req, hu$handle$handle) 7: GET(url) 6: .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) 5: KEGGREST::keggLink("pathway", organism) 4: kegga.default(de = DEGenes, universe = universe, ...) 3: kegga(de = DEGenes, universe = universe, ...) 2: kegga.DGEExact(et, species = "Hs") 1: kegga(et, species = "Hs") > sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale:  LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252  LC_MONETARY=English_Australia.1252 LC_NUMERIC=C  LC_TIME=English_Australia.1252 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  edgeR_3.12.0 limma_3.26.3 loaded via a namespace (and not attached):  locfit_1.5-9.1 IRanges_2.4.6 lattice_0.20-33  png_0.1-7 Biostrings_2.38.3 grid_3.2.0  R6_2.1.1 stats4_3.2.0 magrittr_1.5  httr_1.0.0 zlibbioc_1.16.0 stringi_1.0-1  curl_0.9.4 XVector_0.10.0 S4Vectors_0.8.5  splines_3.2.0 tools_3.2.0 stringr_1.0.0  parallel_3.2.0 BiocGenerics_0.16.1 KEGGREST_1.10.0
EDIT: From the traceback output, it should be a problem of KEGGREST package. I added it into tag.