[R-sig-Geo] Strange Rgdal compile error (possibly three)

Wed Nov 5 16:38:33 CET 2014

Hi,
I have the same problem with MacOS x maverick.

I had installed the GDAL_Complete-1.11.dmg but it looks it can't find it 
when running this R CMD?
Nonehteless $ echo $PATH
/Library/Frameworks/Python.framework/Versions/3.3/bin:/Library/Frameworks/GDAL.framework/Programs:/usr/texbin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin

console$ R CMD install rgdal_0.9-1.tar.gz

* installing to library '/Users/lgzdl/Library/R/3.1/library'
* installing *source* package 'rgdal' ...
** package 'rgdal' successfully unpacked and MD5 sums checked
configure: CC: clang
configure: CXX: clang++
configure: rgdal: 0.9-1
checking for /usr/bin/svnversion... yes
configure: svn revision: 518
configure: gdal-config: gdal-config
checking gdal-config usability... yes
configure: GDAL: 1.11.1
checking GDAL version >= 1.6.3... yes
checking GDAL version < 2... yes
checking for gcc... clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking gdal.h usability... yes
checking gdal.h presence... yes
checking for gdal.h... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
*ld: framework not found GDAL*
clang: error: linker command failed with exit code 1 (use -v to see 
invocation)
ld: framework not found GDAL
clang: error: linker command failed with exit code 1 (use -v to see 
invocation)
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
ERROR: configuration failed for package 'rgdal'

On 30/10/2014 18:14, Paul hewson wrote:
> I'm trying to install rgdal on Kubuntu 14.04 and R 3.1.1; I have spent a lot
> of time following up various online suggestions for the problems I think I'm
> seeing but am currently rather baffled.   I'd be very grateful for a hint.
> I am using R CMD INSTALL ......
>
> libgdal1-dev is installed, mariadb is installed, and armadillo/poppler etc
> are installed (although ld can't find them).
>
> To date, I have followed
> - Old postings about GDALAllRegister not found
> http://stackoverflow.com/questions/15569720/install-rgdal-library-in-rstudio-gdalallregister-not-found-in-libgdal
> - not relevant here (I have compiliers)
> - GDAL stuff on the amadillo / poppler missing (they are not - there might
> be some ubuntu packaging issue here if I'm reading launchpad right)
> https://bugs.launchpad.net/ubuntu/+source/gdal/+bug/1194082
> - There is some stuff on MySQL / mariadb compatibility.
> https://github.com/Homebrew/homebrew/issues/32973
>
> If anyone has any hints about what I should do next I'd be really grateful.
> For example, I don't know whether to knock out mariadb to see whether/how
> that helps, but there seem to be orthogonal warnings.
>
>
> checking gdal: linking with --libs only... no
> checking gdal: linking with --libs and --dep-libs... no
>
> /usr/lib/libgdal.so: undefined reference to `mysql_error at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `mysql_options at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `mysql_fetch_lengths at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `mysql_real_connect at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to `mysql_query at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `mysql_free_result at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to `my_init at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `mysql_field_seek at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `mysql_num_rows at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `mysql_num_fields at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to `mysql_close at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `mysql_field_count at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `free_defaults at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to `mysql_init at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `mysql_fetch_row at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `mysql_fetch_field at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to `mysql_errno at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `mysql_insert_id at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `mysql_use_result at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `mysql_store_result at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `load_defaults at libmysqlclient_18'
> /usr/lib/libgdal.so: undefined reference to
> `mysql_affected_rows at libmysqlclient_18'
> collect2: error: ld returned 1 exit status
>
> /usr/bin/ld: cannot find -larmadillo
> /usr/bin/ld: cannot find -lproj
> /usr/bin/ld: cannot find -lpoppler
> /usr/bin/ld: cannot find -lfreexl
> /usr/bin/ld: cannot find -lepsilon
> /usr/bin/ld: cannot find -lkmldom
> /usr/bin/ld: cannot find -lkmlbase
> /usr/bin/ld: cannot find -lkmlengine
> /usr/bin/ld: cannot find -lkmlconvenience
> /usr/bin/ld: cannot find -lminizip
> /usr/bin/ld: cannot find -luriparser
> collect2: error: ld returned 1 exit status
>
> configure: Install failure: compilation and/or linkage problems.
>
> configure: error: GDALAllRegister not found in libgdal.
>
>
>
>
> --
> View this message in context: http://r-sig-geo.2731867.n2.nabble.com/Strange-Rgdal-compile-error-possibly-three-tp7587374.html
> Sent from the R-sig-geo mailing list archive at Nabble.com.
>
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-- 
Dr Didier G. Leibovici
    d-d'ye    ley-bow-v-c
Senior Research Fellow
Geocomputational Modelling & Geospatial Statistics
Nottingham Geospatial Institute
University of Nottingham, UK
+44 (0)115 84 13924
http://www.nottingham.ac.uk/ngi/people/didier.leibovici
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