(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
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