Installation issues

[shr...@umich.edu]

Hey,

I am having the same old methylKit installation problem.

I am using a Bioconductor 3.0v on a 3.1.3v R in a Linux-OS. I encountered the following error when I ran the installation code:

> download.file("http://methylkit.googlecode.com/files/methylKit_0.9.2.tar.gz",destfile="methylKit_0.9.2.tar.gz")

trying URL 'http://methylkit.googlecode.com/files/methylKit_0.9.2.tar.gz'

Content type 'application/x-gzip; charset=binary' length 1095583 bytes (1.0 MB)

downloaded 1.0 MB

> install.packages("methylKit_0.9.2.tar.gz",repos=NULL,type="source")

Installing package into ‘C:/Users/shriya/Documents/R/win-library/3.2’

(as ‘lib’ is unspecified)

* installing *source* package 'methylKit' ...

** R

** data

** exec

** inst

** preparing package for lazy loading

Error : objects 'DataFrame', 'Rle', 'elementMetadata', 'elementMetadata<-' are not exported by 'namespace:IRanges'

ERROR: lazy loading failed for package 'methylKit'

* removing 'C:/Users/shriya/Documents/R/win-library/3.2/methylKit'

Warning messages:

1: running command '"C:/PROGRA~1/R/R-32~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\shriya\Documents\R\win-library\3.2" "methylKit_0.9.2.tar.gz"' had status 1 

2: In install.packages("methylKit_0.9.2.tar.gz", repos = NULL, type = "source") :

  installation of package ‘methylKit_0.9.2.tar.gz’ had non-zero exit status

Looking at the solutions suggested previously for the same issues, I also tried installing the R3.2v and used the BioConductor 3.1v. The problem still persists. Could you please help me in solving this issue. Thank you.

[Altuna Akalin]

Hi, current suggested method of installation is to use install_github. see https://code.google.com/p/methylkit/#Installation

Best,

Altuna

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[shr...@umich.edu]

Thank you very much. I figured there was also a problem with loading RCurl and devtools packages. I installed them separately and it works in the latest version. Although Iam still unable to get devtools and RCurl loaded in the R3.1.3, BioC 3.1 version. 

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