|
|
|
|
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
|
|
|
https://askubuntu.com/questions/360329/error-cannot-run-c-compiled-programs-if-you-meant-to-cross-compile-use-hostmight 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
|
|
|
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.comhttp://www.sarahgoslee.comhttp://www.functionaldiversity.org [[alternative HTML version deleted]]
_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo
|
|
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/0000-0003-2392-6140https://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
|
|
|
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
|
|
|
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
|
|
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/0000-0003-2392-6140https://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
|
|
|
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
|
|
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
|
|
|
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
|
|
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
>>>
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Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
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