On Nov 15, 2011, at 8:36 PM, Dan Tenenbaum wrote: > Hi all, > > 2011/11/15 Hervé Pagès <hpa...@fhcrc.org>: >> 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. >> >>> >>> 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. >> > > This is fixed now. At the end of our next build cycle (about 1PM > tomorrow, Wednesday, Seattle time), xcms 1.30.1 will be available > which is once again built against the static netcdf library (version > 4.0.1) that Simon provides on his site. Other BioC packages that use > netcdf (flowWorkspace and mzR) will also be fixed. > > Riccardo, this means that all you have to do is wait until the new > package is available and then: > source("http://bioconductor.org/biocLite.R") > biocLite("xcms") > library(xcms) > > You will not need to compile anything. I just tested this on a Mac > without netcdf or any compilers and it worked fine. > > Simon: I will be asking for your help but I want to make sure I have > all my ducks in a row first. I want first to be able to build things > exactly right, then I can know that I am giving you the right thing. > That is taking a bit more time than I'd like. > > Briefly, the package in question needs netcdf (must be version 4.1.3) > to be linked against hdf5 which in turn needs to link to zlib. > I will contact you when I am able to create a static version of this > that allows this package to compile. >
Note that in libs there is static hdf5 and netcdf 4.1.1 (which uses hdf5), so the only issue is that the package needs 4.1.3 and not 4.1.1 -- I wonder why since it's just a patch release ... Cheers, Simon > Thanks for your help. > Dan > > > > >> 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 >>>>>> R-SIG-Mac@r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> R-SIG-Mac mailing list >>>>> R-SIG-Mac@r-project.org >>>>> 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: hpa...@fhcrc.org >>>> Phone: (206) 667-5791 >>>> Fax: (206) 667-1319 >>>> >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac@r-project.org >>>> 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: hpa...@fhcrc.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac