rgdal installation on Fedora 28

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
11 messages Options
Reply | Threaded
Open this post in threaded view
|

rgdal installation on Fedora 28

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.

> 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</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

--
Sarah Goslee
http://www.functionaldiversity.org

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal installation on Fedora 28

Ista Zahn-2
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 <[hidden email]> 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</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
>
> --
> Sarah Goslee
> http://www.functionaldiversity.org
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal installation on Fedora 28

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 <[hidden email]> wrote:

>
> 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 <[hidden email]>
> 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</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
> >
> > --
> > Sarah Goslee
> > http://www.functionaldiversity.org
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > [hidden email]
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
--
Sarah Goslee
http://www.stringpage.com
http://www.sarahgoslee.com
http://www.functionaldiversity.org

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal installation on Fedora 28

Roger Bivand
Administrator
On Fri, 15 Jun 2018, Sarah Goslee wrote:

> 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?

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


>
> Sarah
>
>
> On Fri, Jun 15, 2018 at 4:31 PM Ista Zahn <[hidden email]> wrote:
>
>>
>> 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 <[hidden email]>
>> 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</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
>>>
>>> --
>>> Sarah Goslee
>>> http://www.functionaldiversity.org
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> [hidden email]
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: [hidden email]
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
Reply | Threaded
Open this post in threaded view
|

Re: rgdal installation on Fedora 28

R-sig-geo mailing list
In reply to this post by Sarah Goslee
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 <[hidden email]> 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</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

--
Sarah Goslee
http://www.functionaldiversity.org

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo 
        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal installation on Fedora 28

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], [hidden email])
 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 <
[hidden email]> 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 <
> [hidden email]> 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</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
>
> --
> Sarah Goslee
> http://www.functionaldiversity.org
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal installation on Fedora 28

Roger Bivand
Administrator
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], [hidden email])
> 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 <
> [hidden email]> 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 <
>> [hidden email]> 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</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
>>
>> --
>> Sarah Goslee
>> http://www.functionaldiversity.org
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> [hidden email]
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: [hidden email]
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
Reply | Threaded
Open this post in threaded view
|

Re: rgdal installation on Fedora 28

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 <[hidden email]> 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], [hidden email])
>> 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 <
>> [hidden email]> 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 <
>>> [hidden email]> 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</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
>>>

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal installation on Fedora 28

Roger Bivand
Administrator
Sarah, thanks for checking and reporting back!

Roger

Roger Bivand
Norwegian School of Economics
Bergen, Norway



Fra: Sarah Goslee
Sendt: søndag 17. juni, 14.50
Emne: Re: [R-sig-Geo] rgdal installation on Fedora 28
Til: Roger Bivand
Kopi: Colin Rundel, [hidden email]


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], [hidden email]) >> 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 < >> [hidden email]> 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 < >>> [hidden email]> 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 >>>


        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
Reply | Threaded
Open this post in threaded view
|

Re: rgdal installation on Fedora 28

Barry Rowlingson
In reply to this post by Sarah Goslee
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 <[hidden email]>
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 <[hidden email]> 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], [hidden email])
> >> 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 <
> >> [hidden email]> 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 <
> >>> [hidden email]> 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</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
> >>>
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Reply | Threaded
Open this post in threaded view
|

Re: rgdal installation on Fedora 28

Roger Bivand
Administrator
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: søndag 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 <[hidden email]<mailto:[hidden email]>> 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 <[hidden email]<mailto:[hidden email]>> 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<http://configure.ac>:
>>
>> diff --git a/configure.ac<http://configure.ac> b/configure.ac<http://configure.ac>
>> index 8ff72be..ab4c772 100644
>> --- a/configure.ac<http://configure.ac>
>> +++ b/configure.ac<http://configure.ac>
>> @@ -3,6 +3,8 @@ define([pkgversion], esyscmd([sh -c "grep Version:
>> DESCRIPTION | cut -d' ' -f2 |
>> AC_INIT(rgdal, [pkgversion], [hidden email]<mailto:[hidden email]>)
>> 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 <
>> [hidden email]<mailto:[hidden email]>> 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 <
>>> [hidden email]<mailto:[hidden email]>> 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</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
>>>

_______________________________________________
R-sig-Geo mailing list
[hidden email]<mailto:[hidden email]>
https://stat.ethz.ch/mailman/listinfo/r-sig-geo




        [[alternative HTML version deleted]]

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway