Dan, static hdf5-1.8.8 and netcdf-4.1.3 are now in http://r.research.att.com/libs/ (and also on the CRAN machine).
Cheers, Simon On Nov 15, 2011, at 9:40 PM, Simon Urbanek wrote: > > On Nov 15, 2011, at 8:36 PM, Dan Tenenbaum wrote: > >> Hi all, >> >> 2011/11/15 Hervé Pagès <[email protected]>: >>> 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 >>>>>>> [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 >>> >> >> > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
