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

Simon Urbanek simon.urbanek at r-project.org
Wed Nov 16 04:26:13 CET 2011 

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 <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
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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
>>>>> 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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