Difficulty installing keggrest and httr in R

Question

[ejmcmaho]

Hi,

I am attempting to do a pathway analysis using KEGG on my results from DESeq2. I have run into some trouble installing the keggrest package from biocLite in R. The error i am getting from Rstudio is:

> library(KEGGREST)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘httr’
Error: package or namespace load failed for ‘KEGGREST’

I thought that the thing to do would be to install the httr package, but when I tried to do that I came across the following error:

> install.packages("httr")
trying URL 'http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.1/httr_0.6.1.tgz'
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.1/httr_0.6.1.tgz'
Warning in install.packages :
  download of package ‘httr’ failed

Any guidance would be greatly appreciated.

Thanks,

Evan

Answer 1

[Deepak Tanwar]

Update R. You are using an old version. Maybe after updating, your problem get resolved. I didn't face any problem in installing httr and KEGGREST.

Answer 2

[Arjun]

Hi Evan,

Try iPathwayGuide for your DESeq2 data. It will take your input file as it is and perform pathway analysis with KEGG as reference database. It will also perform GO, disease, predicted miRNAs, etc. analysis. It's pathway analysis method combines enrichment with perturbation that considers additional information about the genes and their interactions in each pathway to identify significantly impacted ones. The method (Impact Analysis) was published in Genome Research and is known to avoid false positive results. You can register and analyze your data for free but unless you have a subscription, you will only get a free 72 hours preview. There are various deals for academic researchers that give up to 65% discount on subscriptions. You can send an email at arjun@advaitabio(dot)com for more information.

Thanks,
Arjun

[Ram]

I do not think we should encourage commercial plugs, should we, Istvan Albert, Devon Ryan?

[Arjun]

Hi Ram,

It can be used as a free resource and the analysis method could be something interesting for the community.

Best,
Arjun

[Ram]

Is the analysis method open source? Do I have access to all of it in a FOSS fashion? I'm quite sure free with strings attached/freemium is not a working model for the community.

In your previous posts recommending it, the tool was quoted as free. Now, this one has something about a subscription, which is why I raise this exception.

Also, I see a line in the website offering a deal, a single report for $300+. Even with a 65% discount that's in excess of $100. Please tell me how this is not a commercial plug.

EDIT: The tool looks wonderful, and the prospect of creating as many reports as you'd like and picking only the best of them is nice (provided it is still the valid offer, and nothing has changed between when the YouTube video was created and now). But this is still a commercial tool. If only you had a free version for academics, I'm sure your reach would increase.