On Nov 15, 2011, at 10:18 AM, Hervé Pagès wrote: > On 11-11-15 06:26 AM, Simon Urbanek wrote: >> >> On Nov 15, 2011, at 1:29 AM, Hervé Pagès wrote: >> >>> On 11-11-12 11:30 PM, Prof Brian Ripley wrote: >>>> On Sun, 13 Nov 2011, Riccardo Romoli 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?? >>>> >>>> 1) Ask BioC to build the package correctly, or >>>> 2) Build from the sources yourself, preferably using a static netcdf >>>> library. >>>> >>>> People should not be distributing Mac binary packages with hardcoded >>>> paths to dependencies not in the R framework: CRAN does not. >>> >>> Not true. rggobi, Cairo and other Mac binaries on CRAN have hardcoded paths >>> to a bunch of stuff that is not in the R framework. >>> >> >> The above statement is false. >> >> All binaries that involve just libraries (like Cairo) are linked statically >> and have no dependencies (see otool -L). >> >> There are very few exceptions where it doesn't involve a library but an >> entire system: gtk, ggobi and tcltk. For those there is no other option >> since just linking them statically is not sufficient as they rely on other >> external files. For those we provide the binaries for download along with >> the package. > > I'm aware of that and thanks for providing those binaries. > Also thanks for confirming that Ripley's original statement was wrong. >
Just to clarify on my end: in my e-mail "The above statement" was referring to your statement, not Brian's. Whatever you make out of the rest is up to you ;). >> The problem in BioC is that not only it uses unnecessary dependent libraries >> (it didn't use to when you were running it ;)), it doesn't even provide the >> needed dependencies for download with the package. That makes the repository >> useless for the user since the packages simply don't work. > > We used to use your static netcdf from here > > http://r.research.att.com/libs/ > > and that's what we should use. For whatever reason another netcdf > (non-static) ended up being installed on our build machine. We'll fix > that. > Great. Dan mentioned something about more recent netcdf and special handling, but didn't get back to me yet. I can build more recent netcdf if needed, but i need to know what the "specially built" exactly means and which package he was referring to so I can test it. Thanks, Simon > Cheers, > H. > >> >> Cheers, >> Simon >> >> >>>> In >>>> particular, /usr/local/lib need administrative privileges to populate. >>> >>> Note that installing the external stuff needed by rggobi, Cairo etc >>> also requires administrative privileges. >>> >>> Cheers, >>> H. >>> >>>> >>>>> >>>>> Best >>>>> >>>>> 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 >>> >>> >>> -- >>> Hervé Pagès >>> >>> Program in Computational Biology >>> Division of Public Health Sciences >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N, M1-B514 >>> P.O. Box 19024 >>> Seattle, WA 98109-1024 >>> >>> E-mail: [email protected] >>> Phone: (206) 667-5791 >>> Fax: (206) 667-1319 >>> >>> _______________________________________________ >>> R-SIG-Mac mailing list >>> [email protected] >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >>> >> > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: [email protected] > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
