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

[Dan Tenenbaum]

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.

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
>>>>
>>>>
>>>>
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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
>
> _______________________________________________
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