Error while loading packages R 2.14.0

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.

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 <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

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