[R-SIG-Mac] R check error but install ok?!?!

[Prof Brian Ripley]

On Tue, 26 Oct 2010, Benton, Paul wrote:

> 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.

You are doing a multi-arch check but running R under only the one 
arch.  It seems you have a multi-arch install of R (from CRAN?) but do 
not have a multi-arch build of netcdf.

Using R CMD check --no-multiarch *may* be what you want.

You also seem not to be using a clean set of sources: that too may 
give you problems.

>
> 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.

There is no 'new R 2.13.0', and will not be for months.

>
> ######## 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)
>
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>
>> 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))
>
>
>
> 	[[alternative HTML version deleted]]
>
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
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