[R-SIG-Mac] Updating some packages fails

[Ben Tupper]

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> 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>:
> 
>> 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>
>> 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'
>>> 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 <mspinola at una.ac.cr>
>>> 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/>
>>> 
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>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
>> 
> 
> 
> -- 
> *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 <mspinola at una.ac.cr>
> 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/>
> 
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> 
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Ben Tupper
Bigelow Laboratory for Ocean Sciences
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