GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same length as the vector [0]
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@martinhoelzer-8847
Last seen 4.9 years ago
Germany

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

gage pathview • 1.1k views
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Luo Weijun ♦ 1.5k
@luo-weijun-1783
Last seen 25 days ago
United States
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]
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@martinhoelzer-8847
Last seen 4.9 years ago
Germany

Dear Weijun,

thank you for your reply. Now I can settle down a bit, because I was really thinking about what I am doing wrong after several new R installations and different versions testing. :)

Hopefully this can be fixed soon.

Thanks and kind regards,

Martin 

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Dan Tenenbaum ♦ 8.2k
@dan-tenenbaum-4256
Last seen 19 months ago
United States

I received an answer from the KEGG team saying this was a problem on their server that has been fixed now. I verified that http://rest.kegg.jp/link/pathway/hsa now works.

 

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@martinhoelzer-8847
Last seen 4.9 years ago
Germany

Hi, yep, for me it is also working now again. Thanks for the help and the information. 

Cheers,
Martin

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