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

[Riccardo Romoli]

Hello, I try to install  netCDF using:

./configure --prefix=/usr/local/ --disable-netcdf-4
make check install

but the terminal say: configure:

error: no acceptable C compiler found in $PATH

I think I need to install the x developer code with the C compiler. It  
is right?
Best

On 14/nov/11, at 18:57, Dan Tenenbaum wrote:

> 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