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

Tue Nov 15 14:38:00 CET 2011

On Nov 14, 2011, at 10:01 PM, Dan Tenenbaum wrote:

> Hi Simon,
> 
> On Mon, Nov 14, 2011 at 5:34 PM, Simon Urbanek
> <simon.urbanek at r-project.org> wrote:
>> 
>> 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 ...
>> 
> 
> I have asked the package maintainer to have a look and avoid hardcoding library paths.
> 

I don't think this has to do with the package but with the way you build it (at least the current issue).

> For the time being, I don't have a binary of netcdf to send you. Our build system uses a specially built netcdf 4.1.3 because of another package that requires netcdf be built specially from source.

Can you fill me in on the details? I'll be happy to update netcdf when needed - let me know what is the package in question and what are the extra requirements.

Cheers,
Simon

> We'll
> look into special-casing this package so that other packages can use a
> more vanilla, redistributable binary, such as the ones at
> http://r.research.att.com/libs/.
> 
> I'll tell you how to build xcms from source, Riccardo, but you may
> want to check out
> 
> http://metlin.scripps.edu/xcms/
> 
> Which has a browser-based version of xcms (no install required).
> 
> If you still want to build netcdf from source, you will need Xcode.
> You'll also need this Fortran compiler:
> http://r.research.att.com/gfortran-4.2.3.dmg
> Then, download netcdf 4.1.3 from here:
> http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.1.3.tar.gz
> 
> Then do this:
> tar zxf netcdf-4.1.3.tar.gz
> cd netcdf-4.1.3
> ./configure
> make
> sudo make install
> 
> Then you should be able to do this within R:
> source("http://bioconductor.org/biocLite.R")
> biocLite("xcms")
> library(xcms)
> 
> Thanks,
> Dan
> 
> 
> 
> 
> 
>> 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
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> 
>> 
>> 
> 
> 