[R-sig-Geo] Installation of rgdal from CRAN on MACOSX does not work

Roger Bivand Roger.Bivand at nhh.no
Mon Jan 10 20:59:32 CET 2011 

On Sat, 8 Jan 2011, Roger Bivand wrote:

> On Thu, 30 Dec 2010, Roger Bivand wrote:
>
>> On Wed, 29 Dec 2010, Agustin Lobo wrote:
>> 
>>> Roger,
>>> 
>>> But
>>> http://www.kyngchaos.com/files/software/frameworks/rgdal-0.6.29-1.zip
>>> installs with no problems on the same machine and on the same R, would 
>>> that not
>>> discard the possibility of an
>>>> issue of your R installation,
>>>> possibly a multi-architecture issue
>>> 
>>> as you suggest?
>>> 
>>> Please note I'm not personally in a hurry any more as we can work with
>>> the rgdal from kyngchaos.
>> 
>> I will have access to an OSX laptop in a little over a week, and will try 
>> out the CRAN rgdal binaries. Just one report of installation failure isn't 
>> enough. I think that maybe someone on R-sig-mac might know why rgdal.so is 
>> looking for libR.dylib; I don't use OSX, and don't have easy access to such 
>> a machine, which is why I asked for others to comment.
>
> On a Leopard 10.5.8, I see the problem reported by Agus for the CRAN-extra 
> OSX binary rgdal package and freshly installed R 2.12.1 (libR.dylib image not 
> found) in the 32-bit R-GUI, but no problem when running R from the command 
> line. A different problem (mach-o, but wrong architecture) occurs in 64-bit 
> systems, both run from the command line and from R-GUI. Could anyone who 
> wants to follow this up please post to R-sig-Mac, which is the correct list 
> for OSX issues?
>
> Conclusion: on Leopard, the CRAN extras rgdal binary can be used in the 
> 32-bit R application run from the command line, but not otherwise. R 2.12.1 
> installs the 64-bit GUI into the OSX applications toolbar - one needs to open 
> a terminal and type "R", checking that the length of a pointer is 4, to run 
> the version that works.

Prof. Ripley has updated the OSX CRAN extras rgdal binaries to rgdal 
0.6.33, and this new version is confirmed to work under Leopard both 32 
and 64 bit, both GUI and terminal. So the simplest way to install rgdal 
for OSX for the basic set of GDAL and OGR drivers is once again:

setRepositories(ind=1:2)
install.packages("rgdal")

Roger

>
> Roger
>
> PS. The symptoms are:
>
> R64, R-GUI 64
>
>> library(rgdal)
> Loading required package: sp
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object 
> '/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/x86_64/rgdal.so':
>
> dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/x86_64/rgdal.so, 
> 6): no suitable image found.  Did find:
>
> /Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/x86_64/rgdal.so: 
> mach-o, but wrong architecture
> Error: package/namespace load failed for 'rgdal'
>
>
>
> R-GUI 32
>
>> library(rgdal)
> Loading required package: sp
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object 
> '/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i386/rgdal.so':
>
> dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i386/rgdal.so, 
> 6): Library not loaded: libR.dylib
>  Referenced from: 
> /Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i386/rgdal.so
>  Reason: image not found
> Error: package/namespace load failed for 'rgdal'
>
>
>> 
>> Roger
>> 
>>> I just want to report the error to help
>>> having an rgdal installation for MACOSX as
>>> simple as for Windows.
>>> I understand installing from source will always be a bit more
>>> difficult on MACOSX than on linux as there are some basic tools and
>>> libraries that are missing on regular MAC systems that must be
>>> previously installed, but this is not my concern now as I'm focusing
>>> on installations from binaries.
>>> 
>>> Thanks!
>>> 
>>> Agus
>>> 
>>> 
>>> 
>>> 2010/12/29 Roger Bivand <Roger.Bivand at nhh.no>:
>>>> On Wed, 29 Dec 2010, Agustin Lobo wrote:
>>>> 
>>>>> While the installation from
>>>>> http://www.kyngchaos.com/files/software/frameworks/rgdal-0.6.29-1.zip
>>>>> works fine
>>>>> the installation of rgdal from CRAN on MACOSX does not work, despite
>>>>> my previous message that this issue was solved as well
>>>> 
>>>> Please do read the error message:
>>>> 
>>>>>  unable to load shared object
>>>>> 
>>>> '/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i$
>>>>> 
>>>> dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal$
>>>>> 
>>>>> 6): Library not loaded: libR.dylib
>>>>>  Referenced from:
>>>>> 
>>>> /Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i3$
>>>>> 
>>>>>  Reason: image not found
>>>> 
>>>> The image that is not found is libR.dylib, the main R dylib against which
>>>> rgdal.so is linked. So this is still an issue of your R installation,
>>>> possibly a multi-architecture issue (is libR.dylib the i386 version,
>>>> guessing - is libR64.dylib the 64-bit Intel version?).
>>>> 
>>>> Could any OSX users who are using CRAN extra rgdal please help Agus to
>>>> resolve this - it could be that local path modifications are hiding
>>>> libR.dylib, or that R was installed 64-bit only, and the INSTALL_opts=
>>>> argument to install.packages() was not set correctly? I assume that the 
>>>> CRAN
>>>> extras OSX rgdal binary is built against a standard R OSX Intel install,
>>>> which is multi-architecture.
>>>> 
>>>> For a fully updated rgdal, the best combination remains installing the 
>>>> full
>>>> GDAL framework from Kyngchaos, the full tools collection:
>>>> 
>>>> http://r.research.att.com/tools/
>>>> http://cran.r-project.org/bin/macosx/tools
>>>> 
>>>> and install from CRAN source. For a lab, the instructor would rather 
>>>> build a
>>>> local OSX rgdal binary package using the tools collection on one 
>>>> development
>>>> machine with all the correct path variables set (R CMD check rgdal; R CMD
>>>> INSTALL --build rgdal), paying attention to multi-architectures, and
>>>> distribute to lab machines from there. This means that the lab instructor
>>>> can keep rgdal updated if need be, as both Kyngchaos and CRAN extras 
>>>> rgdal
>>>> OSX binary packages typically lag CRAN source.
>>>> 
>>>> Please also note that there are very many very old GDAL binaries out 
>>>> there
>>>> that users pick up and apply, missing all the subsequent bug-fixes and
>>>> improvements - GDAL 1.8.0 release candidate 1 is now out, so we are 
>>>> looking
>>>> at an upgrade to 1.8.0 during January, which Kyngchaos will most likely 
>>>> pick
>>>> up quickly, probably with a current rgdal binary.
>>>> 
>>>> Roger
>>>> 
>>>> 
>>>>> (my confusion was a consequence of mixing both installations in the
>>>>> same session):
>>>>> 
>>>>>> setRepositories(ind=1:2)
>>>>>> install.packages("rgdal")
>>>>> 
>>>>> --- Please select a CRAN mirror for use in this session ---
>>>>> probando la URL
>>>>> 
>>>>> 'http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/leopard/contrib/2.12/rgdal_0.6-31.tgz'
>>>>> Content type 'application/x-gzip' length 10203689 bytes (9.7 Mb)
>>>>> URL abierta
>>>>> ==================================================
>>>>> downloaded 9.7 Mb
>>>>> 
>>>>> 
>>>>> The downloaded packages are in
>>>>> 
>>>>>  /var/folders/iR/iRxOvaG9F10viNoa7WceNU+++TI/-Tmp-//RtmpqIhqn9/downloaded_packages
>>>>>> 
>>>>>> require(rgdal)
>>>>> 
>>>>> Loading required package: rgdal
>>>>> Loading required package: sp
>>>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>>>  unable to load shared object
>>>>> 
>>>>> '/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i386/rgdal.so':
>>>>> 
>>>>>  dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i386/rgdal.so,
>>>>> 6): Library not loaded: libR.dylib
>>>>>  Referenced from:
>>>>> 
>>>>> /Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i386/rgdal.so
>>>>>  Reason: image not found
>>>>>> 
>>>>>> sessionInfo()
>>>>> 
>>>>> R version 2.12.1 (2010-12-16)
>>>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>>>>> 
>>>>> locale:
>>>>> [1] es_ES.UTF-8/es_ES.UTF-8/C/C/es_ES.UTF-8/es_ES.UTF-8
>>>>> 
>>>>> attached base packages:
>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>> 
>>>>> other attached packages:
>>>>> [1] sp_0.9-76
>>>>> 
>>>>> loaded via a namespace (and not attached):
>>>>> [1] grid_2.12.1     lattice_0.19-13 tools_2.12.1
>>>>> 
>>>>> Note that rgdal.so is where it should be:
>>>>> 
>>>>> imac-de-agustin-lobo:~ agustinlobo$ ls -l
>>>>> 
>>>>> /Library/Frameworks/R.framework/Versions/2.12/Resources/library/rgdal/libs/i386/
>>>>> total 15088
>>>>> -rwxr-xr-x  1 agustinlobo  admin  7722168  4 dic 15:57 rgdal.so
>>>>> 
>>>>> This error is not solved by setting the GDAL path.
>>>>> 
>>>>> Agus
>>>>> 
>>>> 
>>>> --
>>>> Roger Bivand
>>>> Economic Geography Section, Department of Economics, Norwegian School of
>>>> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
>>>> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
>>>> e-mail: Roger.Bivand at nhh.no
>>>> 
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> R-sig-Geo at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>> 
>>> 
>> 
>> 
>
>

-- 
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no

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