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

[Dan Tenenbaum]

Hi Riccardo,

On Sun, Nov 13, 2011 at 1:30 PM, Riccardo Romoli <ric.romoli at gmail.com> 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??

Set it to /usr/local.

>
> 2)Why with the older version of R I haven't had no problem??


I'm not sure. I am cc'ing the package maintainer who can perhaps
answer this question for you. Also, perhaps he can change the package
so that as Brian suggests (here:
https://stat.ethz.ch/pipermail/r-sig-mac/2011-November/008781.html),
rather than looking for the netcdf libraries on a hardcoded path, he
can do something like what is done in the CRAN package ncdf (see
http://cran.fhcrc.org/web/packages/ncdf/INSTALL).

Dan


>
> I there a  way in osx to upadate R without to re-install all and not
> installing the GUI app such as in linux??
>
> Riccardo