Resolving installed package updates warning

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

Resolving installed package updates warning

Rich Shepard
   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

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: Resolving installed package updates warning

R help mailing list-2
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" <[hidden email] on behalf of [hidden email]> 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
   
    ______________________________________________
    [hidden email] mailing list -- To UNSUBSCRIBE and more, see
    https://stat.ethz.ch/mailman/listinfo/r-help
    PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    and provide commented, minimal, self-contained, reproducible code.
   

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: Resolving installed package updates warning

Rich Shepard
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

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: Resolving installed package updates warning

R help mailing list-2
Rich,

C++11 is a programming language.

Interestingly, someone else asked for help yesterday with exactly the same error message for rgdal. The subject line was

  "Help reinstalling rgdal (Ubuntu 16.04)"

The suggestions were to visit the mailing lists R-sig-geo and/or R-sig-debian.

It's puzzling to me that the output first says
   configure: C++11 support available
and then later says
  /usr/include/cpl_port.h:187:6: error: #error Must have C++11 or newer.

Maybe the C+11 on the system needs to be a newer version...but this level is pretty much over my head.

I wouldn't even look at the other error messages until that one has been solved.

-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, 9:53 AM, "R-help on behalf of Rich Shepard" <[hidden email] on behalf of [hidden email]> wrote:

    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
   
    ______________________________________________
    [hidden email] mailing list -- To UNSUBSCRIBE and more, see
    https://stat.ethz.ch/mailman/listinfo/r-help
    PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    and provide commented, minimal, self-contained, reproducible code.
   

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: Resolving installed package updates warning

Bert Gunter-2
In reply to this post by Rich Shepard
  What's C++11?

Google it!

-- Bert



Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Fri, Aug 10, 2018 at 9:53 AM, Rich Shepard <[hidden email]>
wrote:

> 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
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posti
> ng-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: Resolving installed package updates warning

Rich Shepard
In reply to this post by R help mailing list-2
On Fri, 10 Aug 2018, MacQueen, Don wrote:

> C++11 is a programming language.

Don,

   That's what I assumed; a version of c++, which is installed here by
default. Perhaps not that verision, but ...

>   configure: C++11 support available
> and then later says
>  /usr/include/cpl_port.h:187:6: error: #error Must have C++11 or newer.

>    configure: CXX: g++
>    configure: C++11 support available
>    checking C++11 support for GDAL >= 2.3.0... yes
>    checking GDAL version >= 1.11.4... yes

   Since the configuration finds C++11 support available and a sufficiently
current version of gdal the warning/errors make no sense to me.

   FWIW, there's no issue compiling/using gdal on slackware; I've done so for
many years.

Rich

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.