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

[Hervé Pagès]

On 11-11-15 07:26 AM, Simon Urbanek wrote:
>
> On Nov 15, 2011, at 10:18 AM, Hervé Pagès wrote:
>
>> 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.
>>
>
> Just to clarify on my end: in my e-mail "The above statement" was referring to your statement, not Brian's. Whatever you make out of the rest is up to you ;).

Just to clarify here too: the fact that you mentioned that there are
exceptions to the "no hardcoded paths to dependencies not in the R
framework" was a useful and honest clarification. So again, thanks!

H.

>
>
>>> 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.
>>
>
> Great. Dan mentioned something about more recent netcdf and special handling, but didn't get back to me yet. I can build more recent netcdf if needed, but i need to know what the "specially built" exactly means and which package he was referring to so I can test it.
>
> Thanks,
> Simon
>
>
>> 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
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
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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
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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
>>
>>
>


-- 
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