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

Simon Urbanek simon.urbanek at r-project.org
Wed Nov 16 03:40:42 CET 2011 

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
>>>>>> _______________________________________________
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>>>>> 
>>>>> 
>>>>> 
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>>>> 
>>>> 
>>>> --
>>>> 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
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>>>> 
>>>> 
>>> 
>> 
>> 
>> --
>> 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
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>> 
> 
>

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