R help - Aug 2018 - Resolving installed package updates warning

Updating installed packages ends with a warning:

Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl =
contriburl,  :
   installation of package ?rgdal? had non-zero exit status

   What steps should I take to correct this?

Rich

I would start by trying to install rgdal by itself, rather than as part of a
"batch" update. As in

  Install.packages('rgdal')

 My expectation is that you will see a more complete error message specific to
rgdal, which presumably will provide a clue or pointer.

-Don

--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
Lab cell 925-724-7509
 
 

?On 8/10/18, 6:48 AM, "R-help on behalf of Rich Shepard"
<r-help-bounces at r-project.org on behalf of rshepard at appl-ecosys.com>
wrote:

       Updating installed packages ends with a warning:
    
    Warning message:
    In install.packages(update[instlib == l, "Package"], l, contriburl
= contriburl,  :
       installation of package ?rgdal? had non-zero exit status
    
       What steps should I take to correct this?
    
    Rich
    
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On Fri, 10 Aug 2018, MacQueen, Don wrote:
> I would start by trying to install rgdal by itself, rather than as part of
> a "batch" update. As in
>
>  Install.packages('rgdal')
Don,

   rgdal was supposed to be installed, but you have a valid point.
> My expectation is that you will see a more complete error message specific
> to rgdal, which presumably will provide a clue or pointer.
   Boy howdy! This is interesting:

* installing *source* package ?rgdal? ...
** package ?rgdal? successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/lib/R
configure: CC: gcc
configure: CXX: g++
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... yes
configure: svn revision: 766
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.3.0
checking C++11 support for GDAL >= 2.3.0... yes
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
In file included from /usr/include/gdal.h:45:0,
                  from gdal_test.cc:1:
/usr/include/cpl_port.h:187:6: error: #error Must have C++11 or newer.
  #    error Must have C++11 or newer.
       ^
In file included from /usr/include/gdal.h:49:0,
                  from gdal_test.cc:1:
/usr/include/cpl_minixml.h:202:47: error: expected template-name before
'<' token
  class CPLXMLTreeCloser: public std::unique_ptr<CPLXMLNode,
CPLXMLTreeCloserDeleter>
                                                ^
/usr/include/cpl_minixml.h:202:47: error: expected '{' before
'<' token
/usr/include/cpl_minixml.h:202:47: error: expected unqualified-id before
'<' token
In file included from /usr/include/ogr_api.h:45:0,
                  from /usr/include/gdal.h:50,
                  from gdal_test.cc:1:
/usr/include/ogr_core.h:79:28: error: expected '}' before end of line
/usr/include/ogr_core.h:79:28: error: expected declaration before end of line
In file included from /usr/include/gdal.h:45:0,
                  from gdal_test.cc:1:
/usr/include/cpl_port.h:187:6: error: #error Must have C++11 or newer.
  #    error Must have C++11 or newer.
       ^
In file included from /usr/include/gdal.h:49:0,
                  from gdal_test.cc:1:
/usr/include/cpl_minixml.h:202:47: error: expected template-name before
'<' token
  class CPLXMLTreeCloser: public std::unique_ptr<CPLXMLNode,
CPLXMLTreeCloserDeleter>
                                                ^
/usr/include/cpl_minixml.h:202:47: error: expected '{' before
'<' token
/usr/include/cpl_minixml.h:202:47: error: expected unqualified-id before
'<' token
In file included from /usr/include/ogr_api.h:45:0,
                  from /usr/include/gdal.h:50,
                  from gdal_test.cc:1:
/usr/include/ogr_core.h:79:28: error: expected '}' before end of line
/usr/include/ogr_core.h:79:28: error: expected declaration before end of line
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
ERROR: configuration failed for package ?rgdal?
* removing ?/usr/lib/R/library/rgdal?
* restoring previous ?/usr/lib/R/library/rgdal?

The downloaded source packages are in
 	?/tmp/RtmpVGIz3Q/downloaded_packages?
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("rgdal") :
   installation of package ?rgdal? had non-zero exit status

   Installed here are:
gcc-5.5.0-i586-1_slack14.2
gcc-g++-5.5.0-i586-1_slack14.2
gcc-gfortran-5.5.0-i586-1_slack14.2
gcc-gnat-5.5.0-i586-1_slack14.2
gcc-go-5.5.0-i586-1_slack14.2
gcc-java-5.5.0-i586-1_slack14.2
gcc-objc-5.5.0-i586-1_slack14.2
gccmakedep-1.0.3-noarch-1

and

gdal-2.3.0-i586-1_SBo

   What's C++11?

Rich