[R-SIG-Mac] Error while loading packages R 2.14.0

[Simon Urbanek]

On Nov 13, 2011, at 4:30 PM, Riccardo Romoli wrote:

> 
> On 13/nov/11, at 02:52, Dan Tenenbaum wrote:
> 
>> On Sat, Nov 12, 2011 at 3:25 PM, Riccardo Romoli <ric.romoli at gmail.com> wrote:
>>> Hi, I have already installed R 2.14.0 and I have some problem to load
>>> several packages, in particular xcms package. I installed it directly from
>>> the GUI and when I try to load it the R I have:
>>> 
>>>> library(xcms)
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>> unable to load shared object
>>> '/Users/riccardoromoli/Library/R/2.14/library/xcms/libs/x86_64/xcms.so':
>>> dlopen(/Users/riccardoromoli/Library/R/2.14/library/xcms/libs/x86_64/xcms.so,
>>> 6): Library not loaded: /usr/local/lib/libnetcdf.7.dylib
>>> Referenced from:
>>> /Users/riccardoromoli/Library/R/2.14/library/xcms/libs/x86_64/xcms.so
>>> Reason: image not found
>>> Inoltre: Warning message:
>>> In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
>>> lib.loc) :
>>> there is no package called ‘digest’
>>> Errore: package/namespace load failed for ‘xcms’
>>>> 
>>> 
>>> I think the error is the absence of ibnetcdf.7.dylib. Do you have any idea
>>> how can I correct this error??
>>> 
>> 
>> xcms requires netcdf and zlib, these can be installed from here:
>> http://www.unidata.ucar.edu/software/netcdf/
>> 
>> The recommended way to install Bioconductor packages is not from the
>> GUI but as follows:
>> 
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("xcms")
>> 
>> Dan
>> 
>> 
>>> Best
>>> 
>>> Riccardo
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
> 
> Thanks Dan,
> I will follow your suggestion, I will install netCDF but I have two further question:
> 
> 1)Following the instruction in the netCDF downloaded foldere I read:
> 
> ./configure --prefix=/home/ed/local --disable-netcdf-4
> make check i
> nstall
> 
> What path(/home/ed/local ) should I set on osx??
> 
> 2)Why with the older version of R I haven't had no problem??
> 
> I there a  way in osx to upadate R without to re-install all and not installing the GUI app such as in linux??
> 

Sure, when you are installing R you have the choice to install what you want, so, obviously, you can choose to not install the R.app. Once you installed R previously, the installer will always perform an upgrade by default.

Cheers,
Simon