Question: Error with R package RontoTools regarding administrator issues downloading updated KEGG data
gravatar for svlachavas
4.1 years ago by
Greece/Athens/National Hellenic Research Foundation
svlachavas740 wrote:

Dear Bioconductor Community,

i tried to implement the ROntoTools R package in my current project, to perform pathway analysis using pathway topology. However, before performing any analysis, i used the function:

updated.kegg <- keggPathwayGraphs("hsa", updateCache = TRUE, verbose = TRUE) # in order to download the latest updated KEGG data for humans

But unfortunately, after a while:

Downloading pathway data:
  |============================================================================| 100%
Parsing pathway data:
  |============================================================================| 100%
Warning message:
In file.remove(tmpDir) :
  cannot remove file 'C:\Users\EFSTAT~1\AppData\Local\Temp\RtmpQhtQhS\ROntoToolsac85e786cf9', reason 'Permission denied'

Im using windows and i naively assume that this has something to do with administration issues, but i run Rstudio every time as an administrator !! Is there a way to overcome this issue ??

My sesssion info: 

R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

[1] LC_COLLATE=Greek_Greece.1253  LC_CTYPE=Greek_Greece.1253   
[3] LC_MONETARY=Greek_Greece.1253 LC_NUMERIC=C                 
[5] LC_TIME=Greek_Greece.1253    

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

other attached packages:
[1] ROntoTools_1.8.1 Rgraphviz_2.12.0 KEGGgraph_1.26.0 XML_3.98-1.3    
[5] KEGGREST_1.8.0   boot_1.3-17      graph_1.46.0    

loaded via a namespace (and not attached):
 [1] IRanges_2.2.7       png_0.1-7           Biostrings_2.36.4   R6_2.1.1           
 [5] stats4_3.2.2        magrittr_1.5        httr_1.0.0          stringi_0.5-5      
 [9] zlibbioc_1.14.0     curl_0.9.3          XVector_0.8.0       S4Vectors_0.6.5    
[13] tools_3.2.2         stringr_1.0.0       parallel_3.2.2      BiocGenerics_0.14.0



ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by svlachavas740
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