Installation problem

[Abdul Kader Kheirallah]

Dear Developers,

I can install the dependencies since I can load them from library but I'm stuck with actually installing GenometriCorr. Here is the error I get in R:

> install.packages('GenometriCorr',repos='http://genometricorr.sourceforge.net/R/',type='source')
Installing package into ‘C:/Users/msxakk/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'http://genometricorr.sourceforge.net/R/src/contrib/GenometriCorr_1.1.14.tar.gz'
Content type 'application/x-gzip' length 2227038 bytes (2.1 Mb)
opened URL
downloaded 2.1 Mb

* installing *source* package 'GenometriCorr' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'GenomeInfoDb::seqlevels' when loading 'GenometriCorr'
Warning: replacing previous import by 'GenomeInfoDb::seqlevels<-' when loading 'GenometriCorr'
Warning: replacing previous import by 'GenomeInfoDb::seqlengths' when loading 'GenometriCorr'
Error : objects 'seqlevels', 'seqlevels<-', 'seqlengths' are not exported by 'namespace:GenomeInfoDb'
ERROR: lazy loading failed for package 'GenometriCorr'
* removing 'C:/Users/msxakk/Documents/R/win-library/3.1/GenometriCorr'
Warning in install.packages :
  running command '"C:/PROGRA~1/R/R-31~1.1/bin/i386/R" CMD INSTALL -l "C:\Users\msxakk\Documents\R\win-library\3.1" C:\Users\msxakk\AppData\Local\Temp\RtmpC0JS0P/downloaded_packages/GenometriCorr_1.1.14.tar.gz' had status 1
Warning in install.packages :
  installation of package ‘GenometriCorr’ had non-zero exit status

The downloaded source packages are in
	‘C:\Users\msxakk\AppData\Local\temp\RtmpC0JS0P\downloaded_packages’

Could you help me sort this problem?

Thanks

[Alexander Favorov]

HI Abdul,
I tried to reproduce the problem, but I got a success:

install.packages('GenometriCorr',repos='http://genometricorr.sourceforge.net/R/',type='source')

trying URL 'http://genometricorr.sourceforge.net/R/src/contrib/GenometriCorr_1.1.14.tar.gz'
Content type 'application/x-gzip' length 2227038 bytes (2.1 MB)
downloaded 2.1 MB

* installing *source* package 'GenometriCorr' ...
** R
** inst
** preparing package for lazy loading

Warning: package 'GenomeInfoDb' was built under R version 3.2.1
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
Warning: package 'GenomeInfoDb' was built under R version 3.2.1
*** arch - x64
Warning: package 'GenomeInfoDb' was built under R version 3.2.1
* DONE (GenometriCorr)

The downloaded source packages are in

‘C:\Users\favorov\AppData\Local\Temp\RtmpUbV753\downloaded_packages’

Let's try to compare the R systems.

My R version in 3.2.0
Did you update biconductor packages with biocLite() call?
What version of GenomeInfoDb do you have installed?

Cheers,
Sasha (Alexander) Favorov

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[Abdul Kader Kheirallah]

Hi Sasha,

My R version is 3.1.1. I will update my R and see if it works. I'll let you know!

Best,
Abdul

[Abdul Kader Kheirallah]

Hi Sasha again,

It worked with new R version... Now it's time to do some data analysis :)

Best,
Abdul