RGDAL installation fail after yum upgrade

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RGDAL installation fail after yum upgrade

David.GIOVANNINI
Dear list members,
I'm tring to install RGDAL on a cluster, but after the update of R packages seems not possible to install it.

Below the error message:

> install.packages("rgdal")
Installing package into '/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5'
(as 'lib' is unspecified)
trying URL 'https://cran.stat.unipd.it/src/contrib/rgdal_1.3-4.tar.gz'
Content type 'application/octet-stream' length 1664774 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package 'rgdal' ...
** package 'rgdal' successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/lib64/R
configure: CC: gcc -m64 -std=gnu99
configure: CXX: g++ -m64
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... yes
configure: svn revision: 766
checking for gdal-config... /bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 1.11.4
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... yes
checking GDAL: /usr/share/gdal/pcs.csv readable... yes
checking proj_api.h presence and usability... yes
./configure: line 2126: test: =: unary operator expected
checking PROJ version >= 4.8.0... yes
checking projects.h presence and usability... yes
/tmp/ccnBOZCl.o: In function `main':
/tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/proj_conf_test2.c:20: undefined reference to `pj_ctx_fclose'
collect2: error: ld returned 1 exit status
./configure: line 2242: ./proj_conf_test2: No such file or directory
checking PROJ.4: epsg found and readable... yes
/tmp/ccu3xNdp.o: In function `main':
/tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/proj_conf_test3.c:20: undefined reference to `pj_ctx_fclose'
collect2: error: ld returned 1 exit status
./configure: line 2301: ./proj_conf_test3: No such file or directory
checking PROJ.4: conus found and readable... yes
configure: Package CPP flags:  -I/usr/include/gdal
configure: Package LIBS:  -L/usr/lib64 -lgdal -lproj
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c OGR_write.cpp -o OGR_write.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c gdal-bindings.cpp -o gdal-bindings.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c init.c -o init.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c inverser.c -o inverser.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c local_stubs.c -o local_stubs.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c ogr_geom.cpp -o ogr_geom.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ogr_polygons.c -o ogr_polygons.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c ogr_proj.cpp -o ogr_proj.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c ogrdrivers.cpp -o ogrdrivers.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c ogrsource.cpp -o ogrsource.o
ogrsource.cpp: In function 'SEXPREC* ogrReadListColumn(OGRLayer*, SEXP, int, int, int)':
ogrsource.cpp:651:12: warning: unused variable 'DINT_MAX' [-Wunused-variable]
     double DINT_MAX = 2251799813685248.0;
            ^
ogrsource.cpp:652:12: warning: unused variable 'DINT_MIN' [-Wunused-variable]
     double DINT_MIN = -2251799813685248.0;
            ^
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c projectit.cpp -o projectit.o
g++ -m64 -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/usr/lib64 -lgdal -lproj -L/usr/lib64/R/lib -lR
installing to /home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rgdal'
    finding HTML links ... done
    CRS-class                               html
    GDALDataset-class                       html
    GDALDriver-class                        html
    GDALMajorObject-class                   html
    GDALRasterBand-class                    html
    GDALReadOnlyDataset-class               html
    GDALReadOnlyDataset-methods             html
    GDALTransientDataset-class              html
    GridsDatums                             html
    RGB2PCT                                 html
    SGDF2PCT                                html
    SpatialGDAL-class                       html
    closeDataset-methods                    html
    displayDataset                          html
    llgrid                                  html
Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/llgrid.Rd:11: file link 'Spatial' in package 'sp' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/llgrid.Rd:16: file link 'gridat' in package 'sp' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/llgrid.Rd:17: file link 'gridat' in package 'sp' does not exist and so has been treated as a topic
    make_EPSG                               html
    nor2k                                   html
    projInfo                                html
    project                                 html
    readGDAL                                html
Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/readGDAL.Rd:136: file link 'flipVertical' in package 'sp' does not exist and so has been treated as a topic
    readOGR                                 html
    showWKT                                 html
    spTransform-methods                     html
    wrappers                                html
    writeOGR                                html
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for 'rgdal' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal/libs/rgdal.so':
  /home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal/libs/rgdal.so: undefined symbol: pj_ctx_fgets
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal'

The downloaded source packages are in
     '/tmp/RtmpXrQsj2/downloaded_packages'
Warning message:
In install.packages("rgdal") :
  installation of package 'rgdal' had non-zero exit status

I have tried several solutions but without any success.

Have you any idea about the problem?

Thanks in advance
David

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Re: RGDAL installation fail after yum upgrade

Roger Bivand
Administrator
On Fri, 21 Sep 2018, [hidden email] wrote:

> Dear list members, I'm tring to install RGDAL on a cluster, but after
> the update of R packages seems not possible to install it.

On a cluster running which very outdated version of which operating
system? How did you install PROJ and GDAL, hopefully from source? How did
you install R, again hopefully from source? If you install from source,
your upstream binaries should only use the limited resources of your
outdated platform; if you install binary packages, those packages will
make brave and possibly untrue assumptions about your platform. It is also
very possible that you have multiple versions of GDAL and/or PROJ on your
systems, and that (parts of) configure and install find different
versions. In particular, at least one version of PROJ does not have
pj_ctx_* file access functions, needed in several places.

If you can't fix your systems (PROJ 4.8.0 was released in 2012, over 6
years ago), use a version of rgdal, GDAL and driver software to match your
vintage. Possibly your compile trains are also very outdated too.

Maintainers cannot be expected to keep current package versions running
smoothly on ancient platforms (although we try to help) without active
contributions from interested users. Provide patches to configure.ac that
work for you and do not have any negative impacts on current systems, or
keep your systems more up to date.

Roger

>
> Below the error message:
>
>> install.packages("rgdal")
> Installing package into '/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5'
> (as 'lib' is unspecified)
> trying URL 'https://cran.stat.unipd.it/src/contrib/rgdal_1.3-4.tar.gz'
> Content type 'application/octet-stream' length 1664774 bytes (1.6 MB)
> ==================================================
> downloaded 1.6 MB
>
> * installing *source* package 'rgdal' ...
> ** package 'rgdal' successfully unpacked and MD5 sums checked
> configure: R_HOME: /usr/lib64/R
> configure: CC: gcc -m64 -std=gnu99
> configure: CXX: g++ -m64
> configure: C++11 support available
> configure: rgdal: 1.3-4
> checking for /usr/bin/svnversion... yes
> configure: svn revision: 766
> checking for gdal-config... /bin/gdal-config
> checking gdal-config usability... yes
> configure: GDAL: 1.11.4
> checking GDAL version >= 1.11.4... yes
> checking gdal: linking with --libs only... yes
> checking GDAL: /usr/share/gdal/pcs.csv readable... yes
> checking proj_api.h presence and usability... yes
> ./configure: line 2126: test: =: unary operator expected
> checking PROJ version >= 4.8.0... yes
> checking projects.h presence and usability... yes
> /tmp/ccnBOZCl.o: In function `main':
> /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/proj_conf_test2.c:20: undefined reference to `pj_ctx_fclose'
> collect2: error: ld returned 1 exit status
> ./configure: line 2242: ./proj_conf_test2: No such file or directory
> checking PROJ.4: epsg found and readable... yes
> /tmp/ccu3xNdp.o: In function `main':
> /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/proj_conf_test3.c:20: undefined reference to `pj_ctx_fclose'
> collect2: error: ld returned 1 exit status
> ./configure: line 2301: ./proj_conf_test3: No such file or directory
> checking PROJ.4: conus found and readable... yes
> configure: Package CPP flags:  -I/usr/include/gdal
> configure: Package LIBS:  -L/usr/lib64 -lgdal -lproj
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c OGR_write.cpp -o OGR_write.o
> g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c gdal-bindings.cpp -o gdal-bindings.o
> gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c init.c -o init.o
> gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c inverser.c -o inverser.o
> gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c local_stubs.c -o local_stubs.o
> g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c ogr_geom.cpp -o ogr_geom.o
> gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ogr_polygons.c -o ogr_polygons.o
> g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c ogr_proj.cpp -o ogr_proj.o
> g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c ogrdrivers.cpp -o ogrdrivers.o
> g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c ogrsource.cpp -o ogrsource.o
> ogrsource.cpp: In function 'SEXPREC* ogrReadListColumn(OGRLayer*, SEXP, int, int, int)':
> ogrsource.cpp:651:12: warning: unused variable 'DINT_MAX' [-Wunused-variable]
>     double DINT_MAX = 2251799813685248.0;
>            ^
> ogrsource.cpp:652:12: warning: unused variable 'DINT_MIN' [-Wunused-variable]
>     double DINT_MIN = -2251799813685248.0;
>            ^
> g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c projectit.cpp -o projectit.o
> g++ -m64 -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/usr/lib64 -lgdal -lproj -L/usr/lib64/R/lib -lR
> installing to /home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal/libs
> ** R
> ** data
> ** inst
> ** byte-compile and prepare package for lazy loading
> ** help
> *** installing help indices
>  converting help for package 'rgdal'
>    finding HTML links ... done
>    CRS-class                               html
>    GDALDataset-class                       html
>    GDALDriver-class                        html
>    GDALMajorObject-class                   html
>    GDALRasterBand-class                    html
>    GDALReadOnlyDataset-class               html
>    GDALReadOnlyDataset-methods             html
>    GDALTransientDataset-class              html
>    GridsDatums                             html
>    RGB2PCT                                 html
>    SGDF2PCT                                html
>    SpatialGDAL-class                       html
>    closeDataset-methods                    html
>    displayDataset                          html
>    llgrid                                  html
> Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/llgrid.Rd:11: file link 'Spatial' in package 'sp' does not exist and so has been treated as a topic
> Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/llgrid.Rd:16: file link 'gridat' in package 'sp' does not exist and so has been treated as a topic
> Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/llgrid.Rd:17: file link 'gridat' in package 'sp' does not exist and so has been treated as a topic
>    make_EPSG                               html
>    nor2k                                   html
>    projInfo                                html
>    project                                 html
>    readGDAL                                html
> Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/readGDAL.Rd:136: file link 'flipVertical' in package 'sp' does not exist and so has been treated as a topic
>    readOGR                                 html
>    showWKT                                 html
>    spTransform-methods                     html
>    wrappers                                html
>    writeOGR                                html
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> Error: package or namespace load failed for 'rgdal' in dyn.load(file, DLLpath = DLLpath, ...):
> unable to load shared object '/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal/libs/rgdal.so':
>  /home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal/libs/rgdal.so: undefined symbol: pj_ctx_fgets
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing '/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal'
>
> The downloaded source packages are in
>     '/tmp/RtmpXrQsj2/downloaded_packages'
> Warning message:
> In install.packages("rgdal") :
>  installation of package 'rgdal' had non-zero exit status
>
> I have tried several solutions but without any success.
>
> Have you any idea about the problem?
>
> Thanks in advance
> David
>
> [[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/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

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Norwegian School of Economics
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Re: RGDAL installation fail after yum upgrade

David.GIOVANNINI
Dear Roger, thanks for your reply.

I know, that this cluster have several problems, at first the pool software.
I'm the maintainer and not the creator, so I have inherited all this problems.

The version of OS is Centos 7.5 and unluckly all the software has been installed
via EPEL repository and not from source.

I have checked all the packages (GDAL v1.11.4, PROJ4 v4.9.1) and seems that
the minimun required version has been satisfied. But on the system I have two
version of PROJ4, the version v4.8.0 ( /usr/bin/proj ) and the version v4.9.1
( /usr/local/bin/proj ).

So can I force the use of the new version of PROJ with some parameters during
the installation of RGDAL?

Thanks in advance for your support.
David

-----Original Message-----
From: Roger Bivand [mailto:[hidden email]]
Sent: Friday, September 21, 2018 12:25 PM
To: GIOVANNINI David (JRC-ISPRA-EXT)
Cc: [hidden email]
Subject: Re: [R-sig-Geo] RGDAL installation fail after yum upgrade

On Fri, 21 Sep 2018, [hidden email] wrote:

> Dear list members, I'm tring to install RGDAL on a cluster, but after
> the update of R packages seems not possible to install it.

On a cluster running which very outdated version of which operating
system? How did you install PROJ and GDAL, hopefully from source? How did
you install R, again hopefully from source? If you install from source,
your upstream binaries should only use the limited resources of your
outdated platform; if you install binary packages, those packages will
make brave and possibly untrue assumptions about your platform. It is also
very possible that you have multiple versions of GDAL and/or PROJ on your
systems, and that (parts of) configure and install find different
versions. In particular, at least one version of PROJ does not have
pj_ctx_* file access functions, needed in several places.

If you can't fix your systems (PROJ 4.8.0 was released in 2012, over 6
years ago), use a version of rgdal, GDAL and driver software to match your
vintage. Possibly your compile trains are also very outdated too.

Maintainers cannot be expected to keep current package versions running
smoothly on ancient platforms (although we try to help) without active
contributions from interested users. Provide patches to configure.ac that
work for you and do not have any negative impacts on current systems, or
keep your systems more up to date.

Roger

>
> Below the error message:
>
>> install.packages("rgdal")
> Installing package into '/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5'
> (as 'lib' is unspecified)
> trying URL 'https://cran.stat.unipd.it/src/contrib/rgdal_1.3-4.tar.gz'
> Content type 'application/octet-stream' length 1664774 bytes (1.6 MB)
> ==================================================
> downloaded 1.6 MB
>
> * installing *source* package 'rgdal' ...
> ** package 'rgdal' successfully unpacked and MD5 sums checked
> configure: R_HOME: /usr/lib64/R
> configure: CC: gcc -m64 -std=gnu99
> configure: CXX: g++ -m64
> configure: C++11 support available
> configure: rgdal: 1.3-4
> checking for /usr/bin/svnversion... yes
> configure: svn revision: 766
> checking for gdal-config... /bin/gdal-config
> checking gdal-config usability... yes
> configure: GDAL: 1.11.4
> checking GDAL version >= 1.11.4... yes
> checking gdal: linking with --libs only... yes
> checking GDAL: /usr/share/gdal/pcs.csv readable... yes
> checking proj_api.h presence and usability... yes
> ./configure: line 2126: test: =: unary operator expected
> checking PROJ version >= 4.8.0... yes
> checking projects.h presence and usability... yes
> /tmp/ccnBOZCl.o: In function `main':
> /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/proj_conf_test2.c:20: undefined reference to `pj_ctx_fclose'
> collect2: error: ld returned 1 exit status
> ./configure: line 2242: ./proj_conf_test2: No such file or directory
> checking PROJ.4: epsg found and readable... yes
> /tmp/ccu3xNdp.o: In function `main':
> /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/proj_conf_test3.c:20: undefined reference to `pj_ctx_fclose'
> collect2: error: ld returned 1 exit status
> ./configure: line 2301: ./proj_conf_test3: No such file or directory
> checking PROJ.4: conus found and readable... yes
> configure: Package CPP flags:  -I/usr/include/gdal
> configure: Package LIBS:  -L/usr/lib64 -lgdal -lproj
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c OGR_write.cpp -o OGR_write.o
> g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c gdal-bindings.cpp -o gdal-bindings.o
> gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c init.c -o init.o
> gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c inverser.c -o inverser.o
> gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c local_stubs.c -o local_stubs.o
> g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c ogr_geom.cpp -o ogr_geom.o
> gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c ogr_polygons.c -o ogr_polygons.o
> g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c ogr_proj.cpp -o ogr_proj.o
> g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c ogrdrivers.cpp -o ogrdrivers.o
> g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c ogrsource.cpp -o ogrsource.o
> ogrsource.cpp: In function 'SEXPREC* ogrReadListColumn(OGRLayer*, SEXP, int, int, int)':
> ogrsource.cpp:651:12: warning: unused variable 'DINT_MAX' [-Wunused-variable]
>     double DINT_MAX = 2251799813685248.0;
>            ^
> ogrsource.cpp:652:12: warning: unused variable 'DINT_MIN' [-Wunused-variable]
>     double DINT_MIN = -2251799813685248.0;
>            ^
> g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/gdal -I"/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/sp/include" -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -c projectit.cpp -o projectit.o
> g++ -m64 -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/usr/lib64 -lgdal -lproj -L/usr/lib64/R/lib -lR
> installing to /home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal/libs
> ** R
> ** data
> ** inst
> ** byte-compile and prepare package for lazy loading
> ** help
> *** installing help indices
>  converting help for package 'rgdal'
>    finding HTML links ... done
>    CRS-class                               html
>    GDALDataset-class                       html
>    GDALDriver-class                        html
>    GDALMajorObject-class                   html
>    GDALRasterBand-class                    html
>    GDALReadOnlyDataset-class               html
>    GDALReadOnlyDataset-methods             html
>    GDALTransientDataset-class              html
>    GridsDatums                             html
>    RGB2PCT                                 html
>    SGDF2PCT                                html
>    SpatialGDAL-class                       html
>    closeDataset-methods                    html
>    displayDataset                          html
>    llgrid                                  html
> Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/llgrid.Rd:11: file link 'Spatial' in package 'sp' does not exist and so has been treated as a topic
> Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/llgrid.Rd:16: file link 'gridat' in package 'sp' does not exist and so has been treated as a topic
> Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/llgrid.Rd:17: file link 'gridat' in package 'sp' does not exist and so has been treated as a topic
>    make_EPSG                               html
>    nor2k                                   html
>    projInfo                                html
>    project                                 html
>    readGDAL                                html
> Rd warning: /tmp/RtmpCB1M7h/R.INSTALL2c944a1d5bee/rgdal/man/readGDAL.Rd:136: file link 'flipVertical' in package 'sp' does not exist and so has been treated as a topic
>    readOGR                                 html
>    showWKT                                 html
>    spTransform-methods                     html
>    wrappers                                html
>    writeOGR                                html
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> Error: package or namespace load failed for 'rgdal' in dyn.load(file, DLLpath = DLLpath, ...):
> unable to load shared object '/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal/libs/rgdal.so':
>  /home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal/libs/rgdal.so: undefined symbol: pj_ctx_fgets
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing '/home/alfielo/R/x86_64-redhat-linux-gnu-library/3.5/rgdal'
>
> The downloaded source packages are in
>     '/tmp/RtmpXrQsj2/downloaded_packages'
> Warning message:
> In install.packages("rgdal") :
>  installation of package 'rgdal' had non-zero exit status
>
> I have tried several solutions but without any success.
>
> Have you any idea about the problem?
>
> Thanks in advance
> David
>
> [[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/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

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Re: RGDAL installation fail after yum upgrade

Rich Shepard
On Fri, 21 Sep 2018, [hidden email] wrote:

> I have checked all the packages (GDAL v1.11.4, PROJ4 v4.9.1) and seems
> that the minimun required version has been satisfied. But on the system I
> have two version of PROJ4, the version v4.8.0 ( /usr/bin/proj ) and the
> version v4.9.1 ( /usr/local/bin/proj ).

David,

   This is the cause of many problems: two different versions of software on
the same host.

> So can I force the use of the new version of PROJ with some parameters
> during the installation of RGDAL?

   Take a look at your $PATH; it's likely that /usr/local/bin/ is checked
before usr/bin/. And different applications using, e.g., proj4, may look for
it in either place. This means that one application finds the 4.9.1 version
while another application finds the 4.8.0 version.

   I recommend that you put all core binaries in /usr/bin (which means moving
4.9.1 from /usr/local/bin/ to /usr/bin/ and keeping in the latter only
software developed locally.

   My network runs Slackware so I don't know how difficult it might be for
you to re-organize your CentOS installations, but making the time to do this
will make life easier for you.

Best regards,

Rich

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Re: RGDAL installation fail after yum upgrade

Roger Bivand
Administrator
On Fri, 21 Sep 2018, Rich Shepard wrote:

> On Fri, 21 Sep 2018, [hidden email] wrote:
>
>>  I have checked all the packages (GDAL v1.11.4, PROJ4 v4.9.1) and seems
>>  that the minimun required version has been satisfied. But on the system I
>>  have two version of PROJ4, the version v4.8.0 ( /usr/bin/proj ) and the
>>  version v4.9.1 ( /usr/local/bin/proj ).
>
> David,
>
>  This is the cause of many problems: two different versions of software on
> the same host.
>
>>  So can I force the use of the new version of PROJ with some parameters
>>  during the installation of RGDAL?
>
>  Take a look at your $PATH; it's likely that /usr/local/bin/ is checked
> before usr/bin/. And different applications using, e.g., proj4, may look for
> it in either place. This means that one application finds the 4.9.1 version
> while another application finds the 4.8.0 version.

Rich: thanks - having multiple versions is indeed a challenge on platforms
where R uses dynamically loaded libraries. On Windows and MacOS, most CRAN
packages with external dependencies are built with static linking (the
*old* way). However, executables are on the PATH, but dynamically loaded
libraries - shared objects - are on LD_LIBRARY_PATH. Try:

echo $LD_LIBRARY_PATH

at the shell prompt, then inside R:

Sys.getenv("LD_LIBRARY_PATH")

and you'll see that R may have made modifications on startup. A typical
trap is also forgetting to run /sbin/ldconfig -v as root after installing
software in /usr/local/lib (and adding /usr/local/lib to a file in
/etc/ld.so.conf.d) so that the shared objects are visible.

The easier route is to have just one version of external software
installed where R can see it; it is harder but possibly on a cluster
necessary to modify LD_LIBRARY_PATH locally and consistently. Also look at
closed sf issues on github; there we stepped back from messing with
LD_LIBRARY_PATH on a general basis.

Hope this helps,

Roger


>
>  I recommend that you put all core binaries in /usr/bin (which means moving
> 4.9.1 from /usr/local/bin/ to /usr/bin/ and keeping in the latter only
> software developed locally.
>
>  My network runs Slackware so I don't know how difficult it might be for
> you to re-organize your CentOS installations, but making the time to do this
> will make life easier for you.
>
> Best regards,
>
> Rich
>
> _______________________________________________
> 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/0000-0003-2392-6140
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