Help reinstalling rgdal (Ubuntu 16.04)

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Help reinstalling rgdal (Ubuntu 16.04)

Alexandra Thorn-3
Hi all,

Following some updates to R that I received via Synaptic Package
Manager on Ubuntu 16.04 (looks like I now have R 3.4.4-1xenial0), I
have been unable to reinstall rgdal, and I need help.

Initially I was getting error messages about dependencies on GDAL
1.11.4, but after following instructions to install GDAL from source
(into my /usr/local directory) I'm now getting a different set of error
messages (see the output error messages posted below my signature).  

I can't tell if this means that I've made a mistake installing GDAL or
if there's some other problem with my setup/configuration.  I really
need rgdal for the analyses I do in R and could use some help figuring
this out.

Thanks,
Alex

> install.packages("rgdal")
Installing package into ‘/home/athorn/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/rgdal_1.3-4.tar.gz'
Content type 'application/x-gzip' length 1664774 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/lib/R
configure: CC: gcc -std=gnu99
configure: CXX: g++
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... no
configure: svn revision: 766
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.3.1
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/local/include/gdal.h:45:0,
                 from gdal_test.cc:1:
/usr/local/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/local/include/gdal.h:49:0,
                 from gdal_test.cc:1:
/usr/local/include/cpl_minixml.h:202:47: error: expected template-name
  before '<' token class CPLXMLTreeCloser: public
  std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^
/usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<'
  token /usr/local/include/cpl_minixml.h:202:47: error: expected
  unqualified-id before '<' token In file included
  from /usr/local/include/ogr_api.h:45:0,
  from /usr/local/include/gdal.h:50, from gdal_test.cc:1:
/usr/local/include/ogr_core.h:79:28: error: expected '}' before end of
  line /usr/local/include/ogr_core.h:79:28: error: expected declaration
  before end of line In file included
  from /usr/local/include/gdal.h:45:0, from gdal_test.cc:1:
/usr/local/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/local/include/gdal.h:49:0,
                 from gdal_test.cc:1:
/usr/local/include/cpl_minixml.h:202:47: error: expected template-name
  before '<' token class CPLXMLTreeCloser: public
  std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^
/usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<'
  token /usr/local/include/cpl_minixml.h:202:47: error: expected
  unqualified-id before '<' token In file included
  from /usr/local/include/ogr_api.h:45:0,
  from /usr/local/include/gdal.h:50, from gdal_test.cc:1:
/usr/local/include/ogr_core.h:79:28: error: expected '}' before end of
  line /usr/local/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 ‘/home/athorn/R/x86_64-pc-linux-gnu-library/3.4/rgdal’

The downloaded source packages are in
        ‘/tmp/RtmpeuSDnj/downloaded_packages’
Warning message:
In install.packages("rgdal") :
  installation of package ‘rgdal’ had non-zero exit status
>

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Re: Help reinstalling rgdal (Ubuntu 16.04)

Jim Lemon-4
Hi Alex,
I don't use Ubuntu, but if I saw that error message I would upgrade my
C++ compiler and try again. With luck, this is what caused the cascade
of errors beneath it.

Jim

On Fri, Aug 10, 2018 at 1:36 AM, Alexandra Thorn
<[hidden email]> wrote:

> Hi all,
>
> Following some updates to R that I received via Synaptic Package
> Manager on Ubuntu 16.04 (looks like I now have R 3.4.4-1xenial0), I
> have been unable to reinstall rgdal, and I need help.
>
> Initially I was getting error messages about dependencies on GDAL
> 1.11.4, but after following instructions to install GDAL from source
> (into my /usr/local directory) I'm now getting a different set of error
> messages (see the output error messages posted below my signature).
>
> I can't tell if this means that I've made a mistake installing GDAL or
> if there's some other problem with my setup/configuration.  I really
> need rgdal for the analyses I do in R and could use some help figuring
> this out.
>
> Thanks,
> Alex
>
>> install.packages("rgdal")
> Installing package into ‘/home/athorn/R/x86_64-pc-linux-gnu-library/3.4’
> (as ‘lib’ is unspecified)
> trying URL 'https://cloud.r-project.org/src/contrib/rgdal_1.3-4.tar.gz'
> Content type 'application/x-gzip' length 1664774 bytes (1.6 MB)
> ==================================================
> downloaded 1.6 MB
>
> * installing *source* package ‘rgdal’ ...
> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
> configure: R_HOME: /usr/lib/R
> configure: CC: gcc -std=gnu99
> configure: CXX: g++
> configure: C++11 support available
> configure: rgdal: 1.3-4
> checking for /usr/bin/svnversion... no
> configure: svn revision: 766
> checking for gdal-config... /usr/local/bin/gdal-config
> checking gdal-config usability... yes
> configure: GDAL: 2.3.1
> 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/local/include/gdal.h:45:0,
>                  from gdal_test.cc:1:
> /usr/local/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/local/include/gdal.h:49:0,
>                  from gdal_test.cc:1:
> /usr/local/include/cpl_minixml.h:202:47: error: expected template-name
>   before '<' token class CPLXMLTreeCloser: public
>   std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^
> /usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<'
>   token /usr/local/include/cpl_minixml.h:202:47: error: expected
>   unqualified-id before '<' token In file included
>   from /usr/local/include/ogr_api.h:45:0,
>   from /usr/local/include/gdal.h:50, from gdal_test.cc:1:
> /usr/local/include/ogr_core.h:79:28: error: expected '}' before end of
>   line /usr/local/include/ogr_core.h:79:28: error: expected declaration
>   before end of line In file included
>   from /usr/local/include/gdal.h:45:0, from gdal_test.cc:1:
> /usr/local/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/local/include/gdal.h:49:0,
>                  from gdal_test.cc:1:
> /usr/local/include/cpl_minixml.h:202:47: error: expected template-name
>   before '<' token class CPLXMLTreeCloser: public
>   std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^
> /usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<'
>   token /usr/local/include/cpl_minixml.h:202:47: error: expected
>   unqualified-id before '<' token In file included
>   from /usr/local/include/ogr_api.h:45:0,
>   from /usr/local/include/gdal.h:50, from gdal_test.cc:1:
> /usr/local/include/ogr_core.h:79:28: error: expected '}' before end of
>   line /usr/local/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 ‘/home/athorn/R/x86_64-pc-linux-gnu-library/3.4/rgdal’
>
> The downloaded source packages are in
>         ‘/tmp/RtmpeuSDnj/downloaded_packages’
> Warning message:
> In install.packages("rgdal") :
>   installation of package ‘rgdal’ had non-zero exit status
>>
>
> ______________________________________________
> [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
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Re: Help reinstalling rgdal (Ubuntu 16.04)

R help mailing list-2
In reply to this post by Alexandra Thorn-3
There are quite a few messages on R-sig-geo about installing rgdal on Ubuntu. Maybe one of them contains your solution?
(I use Mac, so can't help directly)

-Don

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

On 8/9/18, 8:36 AM, "R-help on behalf of Alexandra Thorn" <[hidden email] on behalf of [hidden email]> wrote:

    Hi all,
   
    Following some updates to R that I received via Synaptic Package
    Manager on Ubuntu 16.04 (looks like I now have R 3.4.4-1xenial0), I
    have been unable to reinstall rgdal, and I need help.
   
    Initially I was getting error messages about dependencies on GDAL
    1.11.4, but after following instructions to install GDAL from source
    (into my /usr/local directory) I'm now getting a different set of error
    messages (see the output error messages posted below my signature).  
   
    I can't tell if this means that I've made a mistake installing GDAL or
    if there's some other problem with my setup/configuration.  I really
    need rgdal for the analyses I do in R and could use some help figuring
    this out.
   
    Thanks,
    Alex
   
    > install.packages("rgdal")
    Installing package into ‘/home/athorn/R/x86_64-pc-linux-gnu-library/3.4’
    (as ‘lib’ is unspecified)
    trying URL 'https://cloud.r-project.org/src/contrib/rgdal_1.3-4.tar.gz'
    Content type 'application/x-gzip' length 1664774 bytes (1.6 MB)
    ==================================================
    downloaded 1.6 MB
   
    * installing *source* package ‘rgdal’ ...
    ** package ‘rgdal’ successfully unpacked and MD5 sums checked
    configure: R_HOME: /usr/lib/R
    configure: CC: gcc -std=gnu99
    configure: CXX: g++
    configure: C++11 support available
    configure: rgdal: 1.3-4
    checking for /usr/bin/svnversion... no
    configure: svn revision: 766
    checking for gdal-config... /usr/local/bin/gdal-config
    checking gdal-config usability... yes
    configure: GDAL: 2.3.1
    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/local/include/gdal.h:45:0,
                     from gdal_test.cc:1:
    /usr/local/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/local/include/gdal.h:49:0,
                     from gdal_test.cc:1:
    /usr/local/include/cpl_minixml.h:202:47: error: expected template-name
      before '<' token class CPLXMLTreeCloser: public
      std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^
    /usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<'
      token /usr/local/include/cpl_minixml.h:202:47: error: expected
      unqualified-id before '<' token In file included
      from /usr/local/include/ogr_api.h:45:0,
      from /usr/local/include/gdal.h:50, from gdal_test.cc:1:
    /usr/local/include/ogr_core.h:79:28: error: expected '}' before end of
      line /usr/local/include/ogr_core.h:79:28: error: expected declaration
      before end of line In file included
      from /usr/local/include/gdal.h:45:0, from gdal_test.cc:1:
    /usr/local/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/local/include/gdal.h:49:0,
                     from gdal_test.cc:1:
    /usr/local/include/cpl_minixml.h:202:47: error: expected template-name
      before '<' token class CPLXMLTreeCloser: public
      std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^
    /usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<'
      token /usr/local/include/cpl_minixml.h:202:47: error: expected
      unqualified-id before '<' token In file included
      from /usr/local/include/ogr_api.h:45:0,
      from /usr/local/include/gdal.h:50, from gdal_test.cc:1:
    /usr/local/include/ogr_core.h:79:28: error: expected '}' before end of
      line /usr/local/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 ‘/home/athorn/R/x86_64-pc-linux-gnu-library/3.4/rgdal’
   
    The downloaded source packages are in
    ‘/tmp/RtmpeuSDnj/downloaded_packages’
    Warning message:
    In install.packages("rgdal") :
      installation of package ‘rgdal’ had non-zero exit status
    >
   
    ______________________________________________
    [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
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Re: Help reinstalling rgdal (Ubuntu 16.04)

Jeff Newmiller
Or ask on R-sig-debian...

On August 9, 2018 3:13:38 PM PDT, "MacQueen, Don via R-help" <[hidden email]> wrote:

>There are quite a few messages on R-sig-geo about installing rgdal on
>Ubuntu. Maybe one of them contains your solution?
>(I use Mac, so can't help directly)
>
>-Don
>
>--
>Don MacQueen
>Lawrence Livermore National Laboratory
>7000 East Ave., L-627
>Livermore, CA 94550
>925-423-1062
>Lab cell 925-724-7509
>
>
>
>On 8/9/18, 8:36 AM, "R-help on behalf of Alexandra Thorn"
><[hidden email] on behalf of [hidden email]>
>wrote:
>
>    Hi all,
>    
>    Following some updates to R that I received via Synaptic Package
>    Manager on Ubuntu 16.04 (looks like I now have R 3.4.4-1xenial0), I
>    have been unable to reinstall rgdal, and I need help.
>    
>    Initially I was getting error messages about dependencies on GDAL
>   1.11.4, but after following instructions to install GDAL from source
>(into my /usr/local directory) I'm now getting a different set of error
>  messages (see the output error messages posted below my signature).  
>    
> I can't tell if this means that I've made a mistake installing GDAL or
>   if there's some other problem with my setup/configuration.  I really
> need rgdal for the analyses I do in R and could use some help figuring
>    this out.
>    
>    Thanks,
>    Alex
>    
>    > install.packages("rgdal")
>Installing package into
>‘/home/athorn/R/x86_64-pc-linux-gnu-library/3.4’
>    (as ‘lib’ is unspecified)
>trying URL 'https://cloud.r-project.org/src/contrib/rgdal_1.3-4.tar.gz'
>    Content type 'application/x-gzip' length 1664774 bytes (1.6 MB)
>    ==================================================
>    downloaded 1.6 MB
>    
>    * installing *source* package ‘rgdal’ ...
>    ** package ‘rgdal’ successfully unpacked and MD5 sums checked
>    configure: R_HOME: /usr/lib/R
>    configure: CC: gcc -std=gnu99
>    configure: CXX: g++
>    configure: C++11 support available
>    configure: rgdal: 1.3-4
>    checking for /usr/bin/svnversion... no
>    configure: svn revision: 766
>    checking for gdal-config... /usr/local/bin/gdal-config
>    checking gdal-config usability... yes
>    configure: GDAL: 2.3.1
>    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/local/include/gdal.h:45:0,
>                     from gdal_test.cc:1:
>  /usr/local/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/local/include/gdal.h:49:0,
>                     from gdal_test.cc:1:
> /usr/local/include/cpl_minixml.h:202:47: error: expected template-name
>      before '<' token class CPLXMLTreeCloser: public
>      std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^
>/usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<'
>      token /usr/local/include/cpl_minixml.h:202:47: error: expected
>      unqualified-id before '<' token In file included
>      from /usr/local/include/ogr_api.h:45:0,
>      from /usr/local/include/gdal.h:50, from gdal_test.cc:1:
> /usr/local/include/ogr_core.h:79:28: error: expected '}' before end of
>  line /usr/local/include/ogr_core.h:79:28: error: expected declaration
>      before end of line In file included
>      from /usr/local/include/gdal.h:45:0, from gdal_test.cc:1:
>  /usr/local/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/local/include/gdal.h:49:0,
>                     from gdal_test.cc:1:
> /usr/local/include/cpl_minixml.h:202:47: error: expected template-name
>      before '<' token class CPLXMLTreeCloser: public
>      std::unique_ptr<CPLXMLNode, CPLXMLTreeCloserDeleter> ^
>/usr/local/include/cpl_minixml.h:202:47: error: expected '{' before '<'
>      token /usr/local/include/cpl_minixml.h:202:47: error: expected
>      unqualified-id before '<' token In file included
>      from /usr/local/include/ogr_api.h:45:0,
>      from /usr/local/include/gdal.h:50, from gdal_test.cc:1:
> /usr/local/include/ogr_core.h:79:28: error: expected '}' before end of
>  line /usr/local/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 ‘/home/athorn/R/x86_64-pc-linux-gnu-library/3.4/rgdal’
>    
>    The downloaded source packages are in
>     ‘/tmp/RtmpeuSDnj/downloaded_packages’
>    Warning message:
>    In install.packages("rgdal") :
>      installation of package ‘rgdal’ had non-zero exit status
>    >
>    
>    ______________________________________________
>    [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.

--
Sent from my phone. Please excuse my brevity.

______________________________________________
[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.