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

[Dan Tenenbaum]

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.

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
>>>>>>>
>>>>>>>
>>>>>>>
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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
>>>>
>>>
>>>
>>
>
>