[R-SIG-Mac] Updating some packages fails

[Simon Urbanek]

Manuel,

apologies for the inconvenience - in addition to the original problem the intermediate server that hosts the packages ran out of disk space - it should be all fixed now. Not all packages have been built yet, but a significant portion (packages are built roughly by they reverse-dependencies so most important ones should be through). The back-log should be cleared by next morning.

If you still don't see updated packages, please use
http://r.research.att.com
as your mirror temporarily until all mirrors are synced up.

Thanks,
Simon



> 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/>
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > R-SIG-Mac at r-project.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 
> mspinola10 at gmail.com 
> Teléfono: (506) 8706 - 4662
> Personal website: Lobito de río 
> Institutional website: ICOMVIS