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

[Kasper Daniel Hansen]

On Mon, Nov 14, 2011 at 6:54 PM, Riccardo Romoli <ric.romoli at gmail.com> wrote:
> 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?

Yes.

> 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
>
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