Error while loading packages R 2.14.0
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
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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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