On Nov 14, 2011, at 10:01 PM, Dan Tenenbaum wrote: > 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. >
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 <[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
