Errors at installing rgdal on Debian Buster
Forwarded to list, as Xavier is not subscribed. Roger
On Thu, 14 Sep 2017, Xavier Prudent wrote:
Dear all, I had to recreate the /etc/source.list and could then install homebrew and hence gdal, hence rgdal, that was quite a ride :) but it worked! Thank you for your help! Greetings, Xavier Prudent 2017-09-14 3:26 GMT-04:00 Roger Bivand <Roger.Bivand at nhh.no>:
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) <https://maps.google.com/?q=.1.1-3)+(GCC)&entry=gmail&source=g> 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
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