Martin, I can replicate your problem. Actually several other users had the same issue since yesterday. It used to work fine. The problem can be traced back to keggLink() function of KEGGREST package, and further traced to KEGG REST API Linked entries. Some of this API function is broken. For example, the following line used to get all gene-pathway mapping for human, but retrieves nothing now. path.hsa= KEGGREST::keggLink("pathway", "hsa") Anyway, we will contact KEGG and KEGGREST maintainer on this, see if this can be fixed. Weijun -------------------------------------------- On Tue, 9/22/15, martin.hoelzer [bioc] <noreply@bioconductor.org> wrote: Subject: [bioc] GAGE kegg.gsets function does nor work: 'names' attribute [1] must be the same length as the vector [0] To: luo_weijun@yahoo.com Date: Tuesday, September 22, 2015, 4:19 AM Activity on a post you are following on support.bioconductor.org User martin.hoelzer wrote Question: GAGE kegg.gsets function does nor work: 'names' attribute [1] must be the same length as the vector [0]: Hello,� I am currently installed a new R setup (R-3.2.2) followed by the Bioconductor package source("http://bioconductor.org/biocLite.R") biocLite() and followed by some additonal packages using the biocLite function - gage - pathview Now, when I load gage and pathview and try the following: � kg.mouse = kegg.gsets("mouse") � I get the following error: � Error in names(kg.sets) = paste(species, ks.names, sep = "") :� � 'names' attribute [1] must be the same length as the vector [0] or � Error in FUN(X[[i]], ...) : subscript out of bounds � I dont know what to do now.� � Thanks for your help, Martin Post tags: gage, pathview You may reply via email or visit GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same length as the vector [0]