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
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