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 <[hidden email]> 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? Thanks Agus On Tue, Sep 12, 2017 at 1:49 PM, Roger Bivand <[hidden email]> 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. > > > _______________________________________________ R-sig-Geo mailing list [hidden email] https://stat.ethz.ch/mailman/listinfo/r-sig-geo |
IMHO, debugging a problem like this would become so much easier if you
could provide a docker file that creates the machine you are looking at. Other docker users (like me) could then run it, reproduce your machine, and look at what is going wrong. A set of r-spatial targeting rocker (debian)-based docker images are found here: https://github.com/rocker-org/geospatial a set of ubuntu-based docker files are found here: https://github.com/r-spatial/sf/tree/master/inst/docker On 13/09/17 09:37, 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 <[hidden email]> > 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? > > Thanks > > Agus > > > > On Tue, Sep 12, 2017 at 1:49 PM, Roger Bivand <[hidden email]> 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. >> >> >> > > _______________________________________________ > R-sig-Geo mailing list > [hidden email] > https://stat.ethz.ch/mailman/listinfo/r-sig-geo > Edzer Pebesma Institute for Geoinformatics (ifgi), University of Münster Heisenbergstraße 2, 48149 Münster, Germany; +49 251 83 33081 Journal of Statistical Software: http://www.jstatsoft.org/ Computers & Geosciences: http://elsevier.com/locate/cageo/ _______________________________________________ R-sig-Geo mailing list [hidden email] https://stat.ethz.ch/mailman/listinfo/r-sig-geo |
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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 <[hidden email]> > 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? 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 <[hidden email]> 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: [hidden email] 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 [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 |
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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 <[hidden email]> >> 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 <[hidden email]> 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: [hidden email] 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 [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'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). - 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...) - I will report to r-sig-debian and gdal-dev (please suggest an alternative gdal linst if gdal-dev is not appropriate). I'll keep this list informed. Thanks! Agus On Thu, Sep 14, 2017 at 9:26 AM, Roger Bivand <[hidden email]> 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 <[hidden email]> >>> 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 <[hidden email]> >>> 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: [hidden email] > 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 > [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 |
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In reply to this post by Roger Bivand
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 <[hidden email]>: > >> 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 <[hidden email]> >>>> 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 <[hidden email]> >>>> 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: [hidden email] >> 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: [hidden email] 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 [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 |
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In reply to this post by Agustin Lobo
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). 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...) 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 <[hidden email]> 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 <[hidden email]> >>>> 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 <[hidden email]> >>>> 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: [hidden email] >> 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 >> [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] 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 [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 |
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@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. Correct? Agus On Fri, Sep 15, 2017 at 9:32 AM, Roger Bivand <[hidden email]> 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 <[hidden email]> 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 >>>>> <[hidden email]> >>>>> 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 <[hidden email]> >>>>> 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: [hidden email] >>> 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 >>> [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] > 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 > [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 |
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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@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. 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 <[hidden email]> 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 <[hidden email]> 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 >>>>>> <[hidden email]> >>>>>> 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 <[hidden email]> >>>>>> 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: [hidden email] >>>> 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 >>>> [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] >> 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 >> [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] 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 [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 |
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