[R-SIG-Mac] Updating some packages fails

[Manuel Spínola]

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>:

> Hi,
>
> sf (and many other spatial packages) depend upon gdal (
> 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
>
> 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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>
> --
> *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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>
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
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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 <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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