Dear all,
I'm trying to check the xcms R package under the new R 2.12.0. I can install
the package from the svn code, but when I try to run the check, I get an error
saying that it couldn't load the package. However, I'm able to load xcms and
use the functions (same checked svn code is installed). Any ideas on what I'm
doing wrong would be very helpful.
Thank you,
Paul
PS I know I'm not using the new R 2.13.0 for the check and install but its the
same on devel code as the current stable.
######## checking the svn code
sudo R CMD check xcms
ERROR: sub-architecture 'R' is not installed
* using log directory /Users/hpbenton/xcms/SVN/xcms.Rcheck
* using R version 2.12.0 (2010-10-15)
* using platform: x86_64-apple-darwin9.8.0 (64-bit)
* using session charset: UTF-8
* checking for file xcms/DESCRIPTION ... OK
* this is package xcms version 1.25.1
* checking package name space information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: Rgraphviz
* checking if this is a source package ... WARNING
Subdirectory xcms/src contains object files.
* checking for executable files ... OK
* checking whether package xcms can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
.................
loading checks for arch i386
** checking whether the package can be loaded ... ERROR
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/Users/hpbenton/xcms/SVN/xcms.Rcheck/xcms/libs/i386/xcms.so':
dlopen(/Users/hpbenton/xcms/SVN/xcms.Rcheck/xcms/libs/i386/xcms.so, 6):
Symbol not found: _nc_close
Referenced from: /Users/hpbenton/xcms/SVN/xcms.Rcheck/xcms/libs/i386/xcms.so
Expected in: flat namespace
in /Users/hpbenton/xcms/SVN/xcms.Rcheck/xcms/libs/i386/xcms.so
Error: package/namespace load failed for 'xcms'
Execution halted
It looks like this package has a loading problem: see the messages for
details.
#######Running install
sudo R CMD INSTALL xcms
Password:
* installing to library /Library/Frameworks/R.framework/Resources/library
* installing *source* package xcms ...
** libs
make: *** No rule to make target `fastMatch.o', needed by `xcms.so'. Stop.
*** arch - i386
......................
ld: warning: directory '/sw/lib' following -L not found
ld: warning: in /usr/local/lib/libnetcdf.dylib, file was built for unsupported
file format which is not the architecture being linked (i386)
installing to /Library/Frameworks/R.framework/Resources/library/xcms/libs/i386
*** arch - x86_64
....................
ld: warning: directory '/sw/lib' following -L not found
installing to /Library/Frameworks/R.framework/Resources/library/xcms/libs/x86_64
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (xcms)
###### But running R and installing xcms
###### loading xcms is fine!!!
R version 2.12.0 (2010-10-15)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(xcms)
> setwd("~/xcms/Data/")
xr<-xcmsRaw("CRUCIF_VEG_SAMPLE18_NEG01.CDF")
> xr
An "xcmsRaw" object with 545 mass spectra
Time range: 2.1-720.9 seconds (0-12 minutes)
Mass range: 100.0007-999.9885 m/z
Intensity range: 0-4122
MSn data on 0 mass(es)
with 0 MSn spectra
Profile method: bin
Profile step: 1 m/z (901 grid points from 100 to 1000 m/z)
Memory usage: 1170 MB
> plotSurf(xr, m=c(200,230), rt=c(100,200))
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