[R-sig-Geo] RGDAL installation fail after yum upgrade
D@vid@GIOVANNINI m@ili@g off ext@ec@europ@@eu
D@vid@GIOVANNINI m@ili@g off ext@ec@europ@@eu
Fri Sep 21 15:35:04 CEST 2018
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:Roger.Bivand using nhh.no]
Sent: Friday, September 21, 2018 12:25 PM
To: GIOVANNINI David (JRC-ISPRA-EXT)
Cc: r-sig-geo using r-project.org
Subject: Re: [R-sig-Geo] RGDAL installation fail after yum upgrade
On Fri, 21 Sep 2018, David.GIOVANNINI using ext.ec.europa.eu 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On a cluster running which very outdated version of which operating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outdated platform; if you install binary packages, those packages will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 Possibly your compile trains are also very outdated too.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]]
>
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--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand using nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
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