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

[Simon Urbanek]

On Nov 14, 2011, at 6:54 PM, Riccardo Romoli 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?
> Best

Well, you should really ask the BioC people to either a) fix their build [preferably, as Brian said already] or b) tell you which binary they used to build the package and send it to you. If you try compiling things from sources you'll have to ditch their binaries anyway and you get into the whole mess which binaries are supposed to solve which defeats the point. We are already providing pre-built static netcdf (same as CRAN uses) so it's beyond me why they don't use that ...

Cheers,
Simon



> 
> 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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