[R-sig-Geo] Errors at installing rgdal on Debian Buster
Roger Bivand
Roger.Bivand at nhh.no
Mon Sep 18 09:34:18 CEST 2017
On Mon, 18 Sep 2017, Agustin Lobo wrote:
> rgdal compiles fine on my Debian Testing (Buster) system by removing
> an older pro_api.h file:
>
> 1. As suggested by Roger, I located and removed an older version of
> proj_api.h taht had not been removed when I removed the older proj4
> version:
> $ sudo find / -name proj_api.h
> /usr/local/include/proj_api.h
> /usr/include/proj_api.h
> alobo at debi:~$ sudo rm /usr/local/include/proj_api.h
>
> 2. Then the rgdal installation goes smoothly;
>
> $ R CMD INSTALL rgdal_1.2-8.tar.gz
> .../...
> configure: PROJ.4 version: > 4.8.0
> .../...
>
> (see https://www.dropbox.com/s/9i8rk74k0vk95uc/rgdal2.log?dl=0 for the
> entire output)
>
> 3. Then, in R, rgdal loads with no problems
>
>> require(rgdal)
> Loading required package: rgdal
> Loading required package: sp
> rgdal: version: 1.2-8, (SVN revision 663)
> Geospatial Data Abstraction Library extensions to R successfully loaded
> Loaded GDAL runtime: GDAL 2.2.1, released 2017/06/23
> Path to GDAL shared files: /usr/share/gdal/2.2
> Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
> Path to PROJ.4 shared files: (autodetected)
> Linking to sp version: 1.2-5
>> sessionInfo()
> R version 3.3.3 (2017-03-06)
> Platform: i686-pc-linux-gnu (32-bit)
> Running under: Debian GNU/Linux buster/sid
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> 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
> LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] rgdal_1.2-8 sp_1.2-5
>
> loaded via a namespace (and not attached):
> [1] tools_3.3.3 grid_3.3.3 lattice_0.20-35
>
> 4. Thus I guess all problems were caused by an old gcc compiler +
> leftovers in /usr/local/... directories and that I should
> report to gdal-dev and r-sig-debian that there is actually no problem
> with versions of R. gfal and proj4 in the Debian testing (Buster)
> repos.
Thanks for reporting back! Unless you posted questions on those list, then
your posting here should be sufficient, as the list is searchable.
Roger
>
> Correct?
>
> Agus
>
> On Fri, Sep 15, 2017 at 9:32 AM, Roger Bivand <Roger.Bivand at nhh.no> wrote:
>> On Fri, 15 Sep 2017, Agustin Lobo wrote:
>>
>>> I'm now very confused. It seems to me, in line with what you say, that
>>> I had 2 different
>>> kinds of problems:
>>> - Those derived from upgrading from Debian Stretch to Buster (a
>>> consequence of keeping the system as Debian testing: it is just the
>>> consequence of testing passing from Stretch to Buster as
>>> Stretch becomes Stable) and keeping some older versions of different
>>> components (probably installed by packages outside Debian repos). I
>>> guess these problems have been fixed (although I still do not
>>> understand why the rgdal installation claims I have PROJ4.8, which I
>>> cannot find in my system).
>>
>>
>> Please see whether there are multiple proj_api.h files on your system - if
>> so, rgdal is picking up the first in your search path, but may link against
>> a later *.so, explaining the crashes during the configure run.
>>
>>> - Those derived from Debian packages having been compiled with
>>> different and incompatible options. This is something I cannot fix
>>> myself.
>>>
>>> Therefore:
>>>
>>> - I will go on compiling myself as Roger suggests to regain an
>>> operational system.
>>> - I will try to test on a fresh Buster system (or a docker, which I
>>> will have to find out what it is...)
>>
>>
>> https://github.com/rocker-org/rocker
>> http://dirk.eddelbuettel.com/papers/useR2015_docker.pdf
>>
>> for example.
>>
>>> - I will report to r-sig-debian and gdal-dev (please suggest an
>>> alternative gdal linst if
>>> gdal-dev is not appropriate).
>>>
>>
>> (please keep your heads covered as GEOS and GDAL transition to requiring
>>>
>>> = C++11 ...) Yes, at this stage sharing information is valuable so that
>>
>> others can learn from hard-won experience.
>>
>> Roger
>>
>>
>>> I'll keep this list informed.
>>>
>>> Thanks!
>>>
>>> Agus
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Thu, Sep 14, 2017 at 9:26 AM, Roger Bivand <Roger.Bivand at nhh.no> wrote:
>>>>
>>>> As Edzer said earlier in this thread (and Agus was quite right to post
>>>> rather than contact me directly), reproducing the problem(s) is hard
>>>> without
>>>> access to the specific platform (thread started here):
>>>>
>>>> https://stat.ethz.ch/pipermail/r-sig-geo/2017-September/025974.html
>>>>
>>>> My guesses so far are that the gcc build trains used for R, and for the
>>>> GDAL/PROJ.4 components are not the same, and may not be the same as the
>>>> installed gcc build train used to install rgdal from source. This
>>>> probably
>>>> also affects sf on debian buster (and ubuntu?). It may also affect
>>>> GEOS/rgeos.
>>>>
>>>> The gcc versions do change as platforms are upgraded, so for anything
>>>> using
>>>> C++, the ABI changes will bite hard, and keeping the compiler versions in
>>>> harmony is crucial. The baseline comparison is to install GDAL and its
>>>> dependencies (including PROJ.4) from source (download and unpack source
>>>> tarball, ./configure && make && make install), then probably R from
>>>> source,
>>>> finally rgdal. This has to work, but unpicks the debian/ubuntu packaging
>>>> system on which many rely.
>>>>
>>>> Please also consider taking this up on r-sig-debian, with a reproducible
>>>> example, best in a docker container.
>>>>
>>>> A further thought is that the most frequent cause of trouble on
>>>> debian/ubuntu previously were multiple installs of different versions of
>>>> GDAL, pulled in by different downstream packages, but the current reports
>>>> do
>>>> not suggest this as the cause. Still worth checking, though ...
>>>>
>>>> Roger
>>>>
>>>>
>>>> On Wed, 13 Sep 2017, Roger Bivand wrote:
>>>>
>>>>> On Wed, 13 Sep 2017, Agustin Lobo wrote:
>>>>>
>>>>>> The problem seems to be related to the compiler. I had:
>>>>>> gcc version 5.3.1 20160101 (Debian 5.3.1-5)
>>>>>>
>>>>>> I have now:
>>>>>> gcc version 7.2.0 (Debian 7.2.0-4)
>>>>>>
>>>>>> All weird previus errors are gone but I still have:
>>>>>> configure: PROJ.4 version: 4.8.0
>>>>>> ./configure: line 3725: 8390 Segmentation fault ./proj_conf_test
>>>>>> checking PROJ.4: epsg found and readable... yes
>>>>>> ./configure: line 3800: 8399 Segmentation fault ./proj_conf_test
>>>>>>
>>>>>> and finally
>>>>>>
>>>>>> ** testing if installed package can be loaded
>>>>>> Fatal error: glibc detected an invalid stdio handle
>>>>>> Aborted
>>>>>> ERROR: loading failed
>>>>>> * removing ‘/home/alobo/R/i686-pc-linux-gnu-library/3.3/rgdal’
>>>>>>
>>>>>> Surprisingly, I do have 4.9 installed, not 4.8:
>>>>>>
>>>>>> $ dpkg -s proj-bin
>>>>>> Package: proj-bin
>>>>>> Status: install ok installed
>>>>>> Priority: optional
>>>>>> Section: science
>>>>>> Installed-Size: 125
>>>>>> Maintainer: Debian GIS Project
>>>>>> <pkg-grass-devel at lists.alioth.debian.org>
>>>>>> Architecture: i386
>>>>>> Source: proj
>>>>>> Version: 4.9.3-2
>>>>>>
>>>>>> and
>>>>>> $ proj
>>>>>> Rel. 4.9.3, 15 August 2016
>>>>>> usage: proj [ -bCeEfiIlormsStTvVwW [args] ] [ +opts[=arg] ] [ files ]
>>>>>>
>>>>>> and I cannot find proj_conf_test anywhere:
>>>>>> $ sudo find / -name 'proj_conf_test'
>>>>>> gives no result
>>>>>>
>>>>>> How is the test ./proj_conf_test done so that I can investigate why it
>>>>>> results into PROJ 4.8 instead of 4.9?
>>>>>
>>>>>
>>>>>
>>>>> It is defined in rgdal/configure.ac (line 273 ff.):
>>>>>
>>>>> if test ${proj_version} -ge 480; then
>>>>> [cat > proj_conf_test.c <<_EOCONF
>>>>> #include <stdio.h>
>>>>> #include <proj_api.h>
>>>>> #if PJ_VERSION == 480
>>>>> FILE *pj_open_lib(projCtx, const char *, const char *);
>>>>> #endif
>>>>>
>>>>> int main() {
>>>>> #if PJ_VERSION <= 480
>>>>> FILE *fp;
>>>>> #else
>>>>> PAFile fp;
>>>>> #endif
>>>>> projCtx ctx;
>>>>> ctx = pj_get_default_ctx();
>>>>> fp = pj_open_lib(ctx, "epsg", "rb");
>>>>> if (fp == NULL) exit(1);
>>>>> #if PJ_VERSION <= 480
>>>>> fclose(fp);
>>>>> #else
>>>>> pj_ctx_fclose(ctx, fp);
>>>>> #endif
>>>>> exit(0);
>>>>> }
>>>>> _EOCONF]
>>>>> else
>>>>> [cat > proj_conf_test.c <<_EOCONF
>>>>> #include <stdio.h>
>>>>> #include <proj_api.h>
>>>>> FILE *pj_open_lib(const char *, const char *);
>>>>>
>>>>> int main() {
>>>>> FILE *fp;
>>>>> fp = pj_open_lib("epsg", "rb");
>>>>> if (fp == NULL) exit(1);
>>>>> fclose(fp);
>>>>> exit(0);
>>>>> }
>>>>> _EOCONF]
>>>>> fi
>>>>>
>>>>> and checks that the crucial epsg file is present. It does seem to run,
>>>>> though, which is puzzling - if you read configure.ac, you'll see that I
>>>>> didn't guard against the previous (different) ./proj_conf_test already
>>>>> existing - I'll revise the test names to avoid such false positives in
>>>>> the
>>>>> future.
>>>>>
>>>>> Roger
>>>>>
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Agus
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, Sep 12, 2017 at 1:49 PM, Roger Bivand <Roger.Bivand at nhh.no>
>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>> $ g++ -v
>>>>>>> ...
>>>>>>> gcc version 7.1.1 20170622 (Red Hat 7.1.1-3) (GCC)
>>>>>>>
>>>>>>> in my case on Fedora 26.
>>>>>>>
>>>>>>> Recent versions should be OK, but < 5 may be problematic. If you have
>>>>>>> upgraded in place but not upgraded the compile trains, installing
>>>>>>> r-base
>>>>>>> will not force that.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> Roger Bivand
>>>> Department of Economics, Norwegian School of Economics,
>>>> Helleveien 30, N-5045 Bergen, Norway.
>>>> voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no
>>>> Editor-in-Chief of The R Journal,
>>>> https://journal.r-project.org/index.html
>>>> http://orcid.org/0000-0003-2392-6140
>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> R-sig-Geo at r-project.org
>>>> 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: Roger.Bivand at nhh.no
>> Editor-in-Chief of The R Journal, https://journal.r-project.org/index.html
>> http://orcid.org/0000-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> R-sig-Geo at r-project.org
>> 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: Roger.Bivand at nhh.no
Editor-in-Chief of The R Journal, https://journal.r-project.org/index.html
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
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