[R-SIG-Mac] Error while loading packages R 2.14.0

Riccardo Romoli ric.romoli at gmail.com
Fri Nov 18 12:28:51 CET 2011 

Graces to all for to have given hand to me in the resolution of the  
problem!!!
Now xcms works fine.

Best
Riccardo

On 16/nov/11, at 21:53, Simon Urbanek wrote:

>
> On Nov 16, 2011, at 3:07 PM, Dan Tenenbaum wrote:
>
>> Simo n,
>>
>> On Tue, Nov 15, 2011 at 7:26 PM, Simon Urbanek
>> <simon.urbanek at r-project.org> 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.
>>
>
> No, it's using the wrong flags to link NetCDF - it completely  
> ignores dependencies. It has hard-coded LIBS which is simply wrong.  
> I would suggest the author uses pkg-config to fetch the relevant  
> LIBS, e.g. on the CRAN machine it is
>
> hagal:tmp$ pkg-config --libs netcdf
> -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl
>
> so all the above is simply missing.
>
> Cheers,
> Simon
>
>
>
>> 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 <hpages at 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 at r-project.org
>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> R-SIG-Mac mailing list
>>>>>>>>> R-SIG-Mac at 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: hpages at fhcrc.org
>>>>>>>> Phone:  (206) 667-5791
>>>>>>>> Fax:    (206) 667-1319
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> R-SIG-Mac mailing list
>>>>>>>> R-SIG-Mac at 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: hpages at fhcrc.org
>>>>>> Phone:  (206) 667-5791
>>>>>> Fax:    (206) 667-1319
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> R-SIG-Mac at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>>
>

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