RGDAL installation fail after yum upgrade

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On a cluster running which very outdated version of which operating 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outdated platform; if you install binary packages, those packages will 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 Possibly your compile trains are also very outdated too.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

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Roger Bivand
Department of Economics, Norwegian School of Economics,
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RGDAL installation fail after yum upgrade

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