[R-sig-Geo] rgdal installation on Fedora 28

Sun Jun 17 17:51:55 CEST 2018

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 <sarah.goslee using gmail.com<mailto:sarah.goslee using gmail.com>> wrote:
I can confirm that the patched R-Forge version of rgdal installs
correctly on my systems with no other change.

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

Sarah

On Sat, Jun 16, 2018 at 5:55 PM, Roger Bivand <Roger.Bivand using nhh.no<mailto:Roger.Bivand using nhh.no>> 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], Roger.Bivand using nhh.no<mailto:Roger.Bivand using nhh.no>)
>> AC_CONFIG_SRCDIR(src/gdal-bindings.cpp)
>>
>> +AC_PROG_CXX()
>> +
>> # find R home and set correct compiler + flags
>> : ${R_HOME=`R RHOME`}
>> if test -z "${R_HOME}"; then
>>
>> rerunning autoconf (also assuming m4/ax_cxx_compile_stdcxx.m4 is added)
>> results in ./configure working for me. I don't have a deep enough
>> understanding of the vagaries of autoconf to know why exactly this is
>> necessary on redhat systems and why this fixes it but at least everything
>> seems to work.
>
>
> Thanks very much, committed to R-forge as revision 758.
>
> Roger
>
>
>>
>> -Colin
>>
>> On Fri, Jun 15, 2018 at 7:29 PM Thiago V. dos Santos via R-sig-Geo <
>> r-sig-geo using r-project.org<mailto:r-sig-geo using r-project.org>> wrote:
>>
>>> The following lines in your config.log:
>>>
>>> /usr/bin/ld: /tmp/cc9pfZ1b.o: relocation R_X86_64_32 against .rodata' can
>>> not be used when making a shared object; recompile with -fPIC
>>>
>>> make me wonder: maybe there is a -fPIC compilation flag lacking for you
>>> platform in the makefile?
>>>
>>> Greetings, -- Thiago V. dos Santos
>>> Postdoctoral Research FellowDepartment of Climate and Space Science and
>>> EngineeringUniversity of Michigan
>>>
>>>     On Friday, June 15, 2018, 3:27:44 PM EDT, Sarah Goslee <
>>> sarah.goslee using gmail.com<mailto:sarah.goslee using gmail.com>> wrote:
>>>
>>>  Hi folks,
>>>
>>> I updated all of my linux computers to Fedora 28, and now can’t install
>>> rgdal.
>>>
>>> I can install sf with no problems, so it doesn't appear to be an issue
>>> with GDAL or with proj.
>>>
>>> I checked with Roger Bivand, the package maintainer, who asked me to
>>> confirm whether I could install sf, to make sure it wasn’t a
>>> dependency issue, and to post the logs online, then ask on the
>>> R-sig-geo mailing list. I’m putting the full problem here, and the
>>> abbreviated version on the mailing list.
>>>
>>> I’d appreciate any thoughts: I rely very heavily on the incredibly
>>> useful rgdal package.
>>>
>>>> sessionInfo()
>>>
>>> R version 3.5.0 (2018-04-23)
>>> Platform: x86_64-redhat-linux-gnu (64-bit)
>>> Running under: Fedora 28 (Workstation Edition)
>>>
>>> Matrix products: default
>>> BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
>>>
>>> locale:
>>>  [1] LC_CTYPE=en_US.UTF-8      LC_NUMERIC=C
>>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>>  [7] LC_PAPER=en_US.UTF-8      LC_NAME=C
>>>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats    graphics  grDevices utils    datasets  methods  base
>>>
>>> loaded via a namespace (and not attached):
>>> [1] compiler_3.5.0 tools_3.5.0</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
R-sig-Geo using r-project.org<mailto:R-sig-Geo using r-project.org>
https://stat.ethz.ch/mailman/listinfo/r-sig-geo

	[[alternative HTML version deleted]]