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rgdal installation on Fedora 28

11 messages · Sarah Goslee, Ista Zahn, Roger Bivand +3 more

Original
Sarah Goslee
# 
Hi folks,

I updated all of my linux computers to Fedora 28, and now can?t install rgdal.

I can install sf with no problems, so it doesn't appear to be an issue
with GDAL or with proj.

I checked with Roger Bivand, the package maintainer, who asked me to
confirm whether I could install sf, to make sure it wasn?t a
dependency issue, and to post the logs online, then ask on the
R-sig-geo mailing list. I?m putting the full problem here, and the
abbreviated version on the mailing list.

I?d appreciate any thoughts: I rely very heavily on the incredibly
useful rgdal package.
R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 28 (Workstation Edition)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0</code>


The install message is:

installing *source* package ?rgdal? ...
** package ?rgdal? successfully unpacked and MD5 sums checked
configure: CC: gcc -m64
configure: CXX: g++ -m64
configure: rgdal: 1.3-2
checking for /usr/bin/svnversion... no
configure: svn revision: 755
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... configure: error: in
`/tmp/RtmpfMGBY5/R.INSTALL66c3b8deddb/rgdal':
configure: error: cannot run C++ compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
ERROR: configuration failed for package ?rgdal?
* removing ?/usr/lib64/R/library/rgdal?
* restoring previous ?/usr/lib64/R/library/rgdal?


The complete information and config.log are posted online at:

http://numberwright.com/2018/06/stuck-on-rgdal/


Any ideas? Or any other information that would be useful?

Thanks!
Sarah
Ista Zahn
# 
https://askubuntu.com/questions/360329/error-cannot-run-c-compiled-programs-if-you-meant-to-cross-compile-use-host
might help.

--Ista
On Fri, Jun 15, 2018 at 3:27 PM, Sarah Goslee <sarah.goslee at gmail.com> wrote:
Sarah Goslee
# 
If you read that whole thread, as far as I can tell it's a permissions
error, possibly due to using an external drive.

I can't see how it would apply to installing an R package from /tmp as
root. Other compiled packages install correctly; rgdal is the only one
giving me this error.

Am I missing something in that thread?

Sarah
On Fri, Jun 15, 2018 at 4:31 PM Ista Zahn <istazahn at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Roger Bivand
    

    

      
      #
    

  


  

      
On Fri, 15 Jun 2018, Sarah Goslee wrote:

        

            

      
      
      
    

        
I agree that it doesn't look like that. The main thread here, mostly OSX, 
was: https://stat.ethz.ch/pipermail/r-sig-geo/2018-June/026622.html, 
earlier https://stat.ethz.ch/pipermail/r-sig-geo/2018-May/026591.html.

That was where the CXX11 test need came from. See also 
https://github.com/OSGeo/gdal/issues/681, but I don't think it is that.

Can you unpack the source tarball, remove lines 41-47 from configure.ac, 
run autoconf to rebuild configure, and see whether removing the test 
helps? This is based on a number of off-list contacts.

Roger

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Thiago V. dos Santos
    

    

      
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The following lines in your config.log:

/usr/bin/ld: /tmp/cc9pfZ1b.o: relocation R_X86_64_32 against .rodata' can not be used when making a shared object; recompile with -fPIC

make me wonder: maybe there is a -fPIC compilation flag lacking for you platform in the makefile?

Greetings,?-- Thiago V. dos Santos
Postdoctoral Research FellowDepartment of Climate and Space Science and EngineeringUniversity of Michigan

        
On Friday, June 15, 2018, 3:27:44 PM EDT, Sarah Goslee <sarah.goslee at gmail.com> wrote:

        
Hi folks,

I updated all of my linux computers to Fedora 28, and now can?t install rgdal.

I can install sf with no problems, so it doesn't appear to be an issue
with GDAL or with proj.

I checked with Roger Bivand, the package maintainer, who asked me to
confirm whether I could install sf, to make sure it wasn?t a
dependency issue, and to post the logs online, then ask on the
R-sig-geo mailing list. I?m putting the full problem here, and the
abbreviated version on the mailing list.

I?d appreciate any thoughts: I rely very heavily on the incredibly
useful rgdal package.

            

      
      
      
    

        
R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 28 (Workstation Edition)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8? ? ? LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8? ? ? ? LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8? ? LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8? ? ? LC_NAME=C
 [9] LC_ADDRESS=C? ? ? ? ? ? ? LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats? ? graphics? grDevices utils? ? datasets? methods? base

loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0</code>


The install message is:

installing *source* package ?rgdal? ...
** package ?rgdal? successfully unpacked and MD5 sums checked
configure: CC: gcc -m64
configure: CXX: g++ -m64
configure: rgdal: 1.3-2
checking for /usr/bin/svnversion... no
configure: svn revision: 755
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... configure: error: in
`/tmp/RtmpfMGBY5/R.INSTALL66c3b8deddb/rgdal':
configure: error: cannot run C++ compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
ERROR: configuration failed for package ?rgdal?
* removing ?/usr/lib64/R/library/rgdal?
* restoring previous ?/usr/lib64/R/library/rgdal?


The complete information and config.log are posted online at:

http://numberwright.com/2018/06/stuck-on-rgdal/


Any ideas? Or any other information that would be useful?

Thanks!
Sarah

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Colin Rundel
    

    

      
      #
    

  


  

      
As I mentioned in the tweet, I was able to fix this on both a Fedora 23 and
Fedora 27 machine by making the following change to configure.ac:

diff --git a/configure.ac b/configure.ac
index 8ff72be..ab4c772 100644
--- a/configure.ac
+++ b/configure.ac
@@ -3,6 +3,8 @@ define([pkgversion], esyscmd([sh -c "grep Version:
DESCRIPTION | cut -d' ' -f2 |
 AC_INIT(rgdal, [pkgversion], Roger.Bivand at nhh.no)
 AC_CONFIG_SRCDIR(src/gdal-bindings.cpp)

+AC_PROG_CXX()
+
 # find R home and set correct compiler + flags
 : ${R_HOME=`R RHOME`}
 if test -z "${R_HOME}"; then

rerunning autoconf (also assuming m4/ax_cxx_compile_stdcxx.m4 is added)
results in ./configure working for me. I don't have a deep enough
understanding of the vagaries of autoconf to know why exactly this is
necessary on redhat systems and why this fixes it but at least everything
seems to work.

-Colin

On Fri, Jun 15, 2018 at 7:29 PM Thiago V. dos Santos via R-sig-Geo <

        
r-sig-geo at r-project.org> wrote:

        

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Roger Bivand
    

    

      
      #
    

  


  

      
On Sat, 16 Jun 2018, Colin Rundel wrote:

        

            

      
      
      
    

        
Thanks very much, committed to R-forge as revision 758.

Roger

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Sarah Goslee
    

    

      
      #
    

  


  

      
I can confirm that the patched R-Forge version of rgdal installs
correctly on my systems with no other change.

Thank you to Roger and Colin, and everyone else who took a look. The R
community is the BEST.

Sarah

        
On Sat, Jun 16, 2018 at 5:55 PM, Roger Bivand <Roger.Bivand at nhh.no> wrote:

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Roger Bivand
    

    

      
      #
    

  


  

      
Sarah, thanks for checking and reporting back!

Roger

Roger Bivand
Norwegian School of Economics
Bergen, Norway



Fra: Sarah Goslee
Sendt: s?ndag 17. juni, 14.50
Emne: Re: [R-sig-Geo] rgdal installation on Fedora 28
Til: Roger Bivand
Kopi: Colin Rundel, r-sig-geo at r-project.org


I can confirm that the patched R-Forge version of rgdal installs correctly on my systems with no other change. Thank you to Roger and Colin, and everyone else who took a look. The R community is the BEST. Sarah On Sat, Jun 16, 2018 at 5:55 PM, Roger Bivand wrote: > On Sat, 16 Jun 2018, Colin Rundel wrote: > >> As I mentioned in the tweet, I was able to fix this on both a Fedora 23 >> and >> Fedora 27 machine by making the following change to configure.ac: >> >> diff --git a/configure.ac b/configure.ac >> index 8ff72be..ab4c772 100644 >> --- a/configure.ac >> +++ b/configure.ac >> @@ -3,6 +3,8 @@ define([pkgversion], esyscmd([sh -c "grep Version: >> DESCRIPTION | cut -d' ' -f2 | >> AC_INIT(rgdal, [pkgversion], Roger.Bivand at nhh.no) >> AC_CONFIG_SRCDIR(src/gdal-bindings.cpp) >> >> +AC_PROG_CXX() >> + >> # find R home and set correct compiler + flags >> : ${R_HOME=`R RHOME`} >> if test -z "${R_HOME}"; then >> >> rerunning autoconf (also assuming m4/ax_cxx_compile_stdcxx.m4 is added) >> results in ./configure working for me. I don't have a deep enough >> understanding of the vagaries of autoconf to know why exactly this is >> necessary on redhat systems and why this fixes it but at least everything >> seems to work. > > > Thanks very much, committed to R-forge as revision 758. > > Roger > > >> >> -Colin >> >> On Fri, Jun 15, 2018 at 7:29 PM Thiago V. dos Santos via R-sig-Geo < >> r-sig-geo at r-project.org> wrote: >> >>> The following lines in your config.log: >>> >>> /usr/bin/ld: /tmp/cc9pfZ1b.o: relocation R_X86_64_32 against .rodata' can >>> not be used when making a shared object; recompile with -fPIC >>> >>> make me wonder: maybe there is a -fPIC compilation flag lacking for you >>> platform in the makefile? >>> >>> Greetings, -- Thiago V. dos Santos >>> Postdoctoral Research FellowDepartment of Climate and Space Science and >>> EngineeringUniversity of Michigan >>> >>> On Friday, June 15, 2018, 3:27:44 PM EDT, Sarah Goslee < >>> sarah.goslee at gmail.com> wrote: >>> >>> Hi folks, >>> >>> I updated all of my linux computers to Fedora 28, and now can?t install >>> rgdal. >>> >>> I can install sf with no problems, so it doesn't appear to be an issue >>> with GDAL or with proj. >>> >>> I checked with Roger Bivand, the package maintainer, who asked me to >>> confirm whether I could install sf, to make sure it wasn?t a >>> dependency issue, and to post the logs online, then ask on the >>> R-sig-geo mailing list. I?m putting the full problem here, and the >>> abbreviated version on the mailing list. >>> >>> I?d appreciate any thoughts: I rely very heavily on the incredibly >>> useful rgdal package. >>> >>>> sessionInfo() >>> >>> R version 3.5.0 (2018-04-23) >>> Platform: x86_64-redhat-linux-gnu (64-bit) >>> Running under: Fedora 28 (Workstation Edition) >>> >>> Matrix products: default >>> BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> loaded via a namespace (and not attached): >>> [1] compiler_3.5.0 tools_3.5.0 >>> >>> >>> The install message is: >>> >>> installing *source* package ?rgdal? ... >>> ** package ?rgdal? successfully unpacked and MD5 sums checked >>> configure: CC: gcc -m64 >>> configure: CXX: g++ -m64 >>> configure: rgdal: 1.3-2 >>> checking for /usr/bin/svnversion... no >>> configure: svn revision: 755 >>> checking whether the C++ compiler works... yes >>> checking for C++ compiler default output file name... a.out >>> checking for suffix of executables... >>> checking whether we are cross compiling... configure: error: in >>> `/tmp/RtmpfMGBY5/R.INSTALL66c3b8deddb/rgdal': >>> configure: error: cannot run C++ compiled programs. >>> If you meant to cross compile, use `--host'. >>> See `config.log' for more details >>> ERROR: configuration failed for package ?rgdal? >>> * removing ?/usr/lib64/R/library/rgdal? >>> * restoring previous ?/usr/lib64/R/library/rgdal? >>> >>> >>> The complete information and config.log are posted online at: >>> >>> http://numberwright.com/2018/06/stuck-on-rgdal/ >>> >>> >>> Any ideas? Or any other information that would be useful? >>> >>> Thanks! >>> Sarah >>>

  
  


  


      

    

    

      
      

        


  

        

      Barry Rowlingson
    

    

      
      #
    

  


  

      
Just a quick note to point out that you can test installations on systems
without having to install such a system by using Docker. Fedora 28 images
are available on Docker Hub.

You have to figure out how to install the toolchain and other components
for building R etc but that helps make a reproducible installation
procedure.

Is everyone doing this already?

Barry


On Sun, Jun 17, 2018 at 2:50 PM, Sarah Goslee <sarah.goslee at gmail.com>
wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Roger Bivand
    

    

      
      #
    

  


  

      
Barry,

No, and it's not that easy. Matching GDAL and PROJ versions, source or binary, multiplies the combinations, and putting aws instances into a box is hard (was missing ldconfig of /usr/local, not rgdal). Docker is always a heavy download, and doesn't work for me on the road and my laptop.

A network of actual users  with problems is arguably as efficient, and includes those with problems in looking for solutions, which is harder for a system solution to do. I for example do not know how to configure R and GDAL versions in a container with Fedora despite doing Dirk's workshop, where we used pre-configured Debian systems.

Somehow people come out of this quite well, don't they?

Just some thoughts,

Roger

Roger Bivand
Norwegian School of Economics
Bergen, Norway



Fra: Barry Rowlingson
Sendt: s?ndag 17. juni, 16.13
Emne: Re: [R-sig-Geo] rgdal installation on Fedora 28
Til: Sarah Goslee
Kopi: Roger Bivand, r-sig-geo


Just a quick note to point out that you can test installations on systems without having to install such a system by using Docker. Fedora 28 images are available on Docker Hub.

You have to figure out how to install the toolchain and other components for building R etc but that helps make a reproducible installation procedure.

Is everyone doing this already?

Barry

        
On Sun, Jun 17, 2018 at 2:50 PM, Sarah Goslee <sarah.goslee at gmail.com<mailto:sarah.goslee at gmail.com>> wrote:

        
I can confirm that the patched R-Forge version of rgdal installs
correctly on my systems with no other change.

Thank you to Roger and Colin, and everyone else who took a look. The R
community is the BEST.

Sarah

        
On Sat, Jun 16, 2018 at 5:55 PM, Roger Bivand <Roger.Bivand at nhh.no<mailto:Roger.Bivand at nhh.no>> wrote:

            

      
      
      
    

        
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