Simo n, On Tue, Nov 15, 2011 at 7:26 PM, Simon Urbanek <[email protected]> wrote: > 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). >
Thanks! So far the package does not compile against that but I've asked the package maintainer to take a look. If you are curious, the package is ncdfFlow (http://bioconductor.org/packages/release/bioc/html/ncdfFlow.html) and the error I get is: checking for nc_def_var_deflate in -lnetcdf... no configure: error: netCDF library not found! ERROR: configuration failed for package 'ncdfFlow' Seems like this might be a symbol from zlib. Dan > 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
