Hi Simon, On Mon, Nov 14, 2011 at 5:34 PM, Simon Urbanek <[email protected]> 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. 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. 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 <[email protected]> >>> wrote: >>>> >>>> On 13/nov/11, at 02:52, Dan Tenenbaum wrote: >>>> >>>>> On Sat, Nov 12, 2011 at 3:25 PM, Riccardo Romoli <[email protected]> >>>>> 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 >>>>>> [email protected] >>>>>> 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 >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> > > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
