[R] non-zero exit status error when install GenomeGraphs

[David Winsemius]

(Caveat: I am not a bioc user.) The error messages suggest that you  
are missing dependencies. I looked at the documentation for  
GenomeGraphs and it does not list any dependencies, but I have no way  
of knowing how careful or knowledgeable the authors may or may not  
have bben when they composed that document. The fact that you are  
posting to the wrong mailing list and are not including what version  
of linux (although there is a hint it may be RedHat5) you are running  
suggests you could be fairly new at this.

Is biocLite the correct function for installing a bioc package? It  
appears it may be, but I'm wondering if there is an argument for  
dependencies as there is in install.packages() that you need to set to  
TRUE? If biocLite has a ,... in its argument list (and the error  
message suggests that it does) then you may get better results with  
the same call with an addition of dependencies=TRUE.

Or you could first install the packages that are reported missing: XML  
and biomaRt, and then try again as you did before.

Links to the bioc mailing lists can be found here:

http://www.bioconductor.org/help/index.html

-- 
David.



On Sep 4, 2010, at 4:07 PM, chen chao wrote:

> Hi,
>
> I am trying to install GenomeGraphs package from bioconductor, but  
> failed by
> a non-zero exit error. From the error message, it seems that there  
> is a
> shared library problem. Any suggestion on fixing it? Thanks so much.
>
>> sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
> [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
> [5] LC_MONETARY=C                  LC_MESSAGES=en_US.iso885915
> [7] LC_PAPER=en_US.iso885915       LC_NAME=C
> [9] LC_ADDRESS=C                   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.10.1
>> source("http://bioconductor.org/biocLite.R")
>    biocLite("GenomeGraphs")Warning messages:
> 1: In safeSource() : Redefining 'biocinstall'
> 2: In safeSource() : Redefining 'biocinstallPkgGroups'
> 3: In safeSource() : Redefining 'biocinstallRepos'
>>    biocLite("GenomeGraphs")
> Using R version 2.10.1, biocinstall version 2.5.11.
> Installing Bioconductor version 2.5 packages:
> [1] "GenomeGraphs"
> Please wait...
>
> Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
>  argument 'lib' is missing: using
> '/cchome/cchen1/R/x86_64-unknown-linux-gnu-li
> brary/2.10'
> trying URL '
> http://www.bioconductor.org/packages/2.5/bioc/src/contrib/GenomeGrap
> hs_1.6.0.tar.gz'
> Content type 'application/x-gzip' length 585078 bytes (571 Kb)
> opened URL
> ==================================================
> downloaded 571 Kb
>
> * installing *source* package 'GenomeGraphs' ...
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared library
> '/apps/rhel5/x86_64/R/R-2.10.1//lib64/R/library/
> XML/libs/XML.so':
>  libxmlsec1.so.1: cannot open shared object file: No such file or  
> directory
> Error : .onLoad failed in 'loadNamespace' for 'XML'
> Error : package 'biomaRt' could not be loaded
> ERROR: lazy loading failed for package 'GenomeGraphs'
> * removing
> '/userhom2/3/cchen1/R/x86_64-unknown-linux-gnu-library/2.10/GenomeGra
> phs'
>
> The downloaded packages are in
>        '/tmp/Rtmp3wsJxw/downloaded_packages'
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package 'GenomeGraphs' had non-zero exit status
>
>
>
>
> -- 
> Chen, Chao
> Psychiatry
> University of Chicago
> 924 E 57th St, Chicago, IL 60637
> U. S. A.
> MOE Key Laboratory of Contemporary Anthropology and Center for
> Evolutionary Biology,
> School of Life Sciences and Institutes of Biomedical Sciences,
> Fudan University
> 220# Handan Road, Shanghai (200433)
> P.R.China
>
> 	[[alternative HTML version deleted]]
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius, MD
West Hartford, CT