[R-SIG-Mac] Updating some packages fails

[Duncan Murdoch]

On 15/01/2018 6:03 PM, Manuel Spínola 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.

Building from source needs more from your system than installing a 
prebuilt binary.  If you aren't willing or able to follow Ben's 
instructions, you'll just have to wait until Simon's binary build makes 
it onto CRAN.

Duncan Murdoch

> 
> 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/>
>>
>> [[alternative HTML version deleted]]
>>
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>>
>> Ben Tupper
>> Bigelow Laboratory for Ocean Sciences
>> 60 Bigelow Drive
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>>
>>
>>
> 
>