[R-SIG-Mac] Updating some packages fails

Ben Tupper btupper at bigelow.org
Tue Jan 16 01:18:52 CET 2018


Hi,

That does sound frustrating - have you tried the following from a terminal (not R console)?

$ which gdal-config
/usr/local/bin/gdal-config

And then from within R?

> Sys.which("gdal-config")
                 gdal-config 
"/usr/local/bin/gdal-config" 


Ben

 
> On Jan 15, 2018, at 6:03 PM, Manuel Spínola <mspinola10 at gmail.com> wrote:
> 
> Thank you very much Ben.
> 
> But I am trying to make an update, not a first time installation.  The older sf version is running fine.
> 
> Manuel
> 
> 2018-01-15 10:40 GMT-06:00 Ben Tupper <btupper at bigelow.org <mailto:btupper at bigelow.org>>:
> Hi,
> 
> sf (and many other spatial packages) depend upon gdal (http://www.gdal.org/ <http://www.gdal.org/>) being installed on your platform.  Your message says it can't find the gdal-config utility, "checking for gdal-config... no".  You can install it following these instructions...
> 
> https://trac.osgeo.org/gdal/wiki/DownloadingGdalBinaries <https://trac.osgeo.org/gdal/wiki/DownloadingGdalBinaries>
> 
> I'm not sure about the other packages you list.
> 
> Cheers,
> Ben
> 
> 
> 
>> On Jan 15, 2018, at 11:25 AM, Manuel Spínola <mspinola10 at gmail.com <mailto:mspinola10 at gmail.com>> wrote:
>> 
>> I am still having problems updating some packages, for example,
>> 
>> sf
>> Hmisc
>> rms
>> mgcv
>> RcmdrMisc
>> 
>> Same messages that I showed in my first email.
>> 
>> Manuel
>> 
>> 
>> 2018-01-11 12:17 GMT-06:00 Simon Urbanek <simon.urbanek at r-project.org <mailto:simon.urbanek at r-project.org>>:
>> 
>>> Manuel,
>>> 
>>> the archiving on CRAN has changed recently which broke the updates so
>>> recently the update for macOS packages have been suspended. Hence some most
>>> recent binaries is not available yet - it should be up by tomorrow.
>>> 
>>> Cheers,
>>> Simon
>>> 
>>> 
>>> 
>>>> On Jan 11, 2018, at 12:26 PM, Manuel Spínola <mspinola10 at gmail.com <mailto:mspinola10 at gmail.com>>
>>> wrote:
>>>> 
>>>> Dear list members,
>>>> 
>>>> When trying updating some packages in MacOS High Sierra 10.13 (R 3.4.2)
>>>> some packages, as "sf", fails:
>>>> 
>>>>> install.packages("sf")
>>>> 
>>>> There is a binary version available but the source version is later:
>>>>  binary source needs_compilation
>>>> sf  0.5-5  0.6-0              TRUE
>>>> 
>>>> Do you want to install from sources the package which needs compilation?
>>>> y/n: y
>>>> 
>>>> installing the source package ‘sf’
>>>> 
>>>> trying URL 'https://cran.rstudio.com/src/contrib/sf_0.6-0.tar.gz <https://cran.rstudio.com/src/contrib/sf_0.6-0.tar.gz>'
>>>> Content type 'application/x-gzip' length 7399611 bytes (7.1 MB)
>>>> ==================================================
>>>> downloaded 7.1 MB
>>>> 
>>>> Warning in strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
>>>> unknown timezone 'default/America/Costa_Rica'
>>>> * installing *source* package ‘sf’ ...
>>>> ** package ‘sf’ successfully unpacked and MD5 sums checked
>>>> configure: CC: clang
>>>> configure: CXX: clang++
>>>> checking for gdal-config... no
>>>> no
>>>> configure: error: gdal-config not found or not executable.
>>>> ERROR: configuration failed for package ‘sf’
>>>> * removing
>>>> ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/sf’
>>>> * restoring previous
>>>> ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/sf’
>>>> Warning in install.packages :
>>>> installation of package ‘sf’ had non-zero exit status
>>>> 
>>>> The downloaded source packages are in
>>>> ‘/private/var/folders/gf/vwlbzml90wv7cs2r4v00wg_m0000gn/T/RtmpbmvcCh/
>>> downloaded_packages’
>>>>> 
>>>> 
>>>> 
>>>> Any solution to this problem?
>>>> 
>>>> Manuel
>>>> 
>>>> --
>>>> *Manuel Spínola, Ph.D.*
>>>> Instituto Internacional en Conservación y Manejo de Vida Silvestre
>>>> Universidad Nacional
>>>> Apartado 1350-3000
>>>> Heredia
>>>> COSTA RICA
>>>> mspinola at una.cr <mailto:mspinola at una.cr> <mspinola at una.ac.cr <mailto:mspinola at una.ac.cr>>
>>>> mspinola10 at gmail.com <mailto:mspinola10 at gmail.com>
>>>> Teléfono: (506) 8706 - 4662
>>>> Personal website: Lobito de río <https://sites.google.com/ <https://sites.google.com/>
>>> site/lobitoderio/>
>>>> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/ <http://www.icomvis.una.ac.cr/>>
>>>> 
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>>>> 
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>>> 
>>> 
>> 
>> 
>> -- 
>> *Manuel Spínola, Ph.D.*
>> Instituto Internacional en Conservación y Manejo de Vida Silvestre
>> Universidad Nacional
>> Apartado 1350-3000
>> Heredia
>> COSTA RICA
>> mspinola at una.cr <mailto:mspinola at una.cr> <mspinola at una.ac.cr <mailto:mspinola at una.ac.cr>>
>> mspinola10 at gmail.com <mailto:mspinola10 at gmail.com>
>> Teléfono: (506) 8706 - 4662
>> Personal website: Lobito de río <https://sites.google.com/site/lobitoderio/ <https://sites.google.com/site/lobitoderio/>>
>> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/ <http://www.icomvis.una.ac.cr/>>
>> 
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>> 
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> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive <https://maps.google.com/?q=60+Bigelow+Drive&entry=gmail&source=g>, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org <http://www.bigelow.org/>
> 
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> 
> 
> 
> 
> 
> -- 
> Manuel Spínola, Ph.D. 
> Instituto Internacional en Conservación y Manejo de Vida Silvestre 
> Universidad Nacional 
> Apartado 1350-3000 
> Heredia 
> COSTA RICA 
> mspinola at una.cr <mailto:mspinola at una.ac.cr> 
> mspinola10 at gmail.com <mailto:mspinola10 at gmail.com> 
> Teléfono: (506) 8706 - 4662
> Personal website: Lobito de río <https://sites.google.com/site/lobitoderio/> 
> Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org

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