[R-sig-Geo] spplot graphics problem
Thomas Adams
tea3rd at gmail.com
Mon Nov 9 00:22:00 CET 2015
Hi Dylan,
I'm using ./configure without any options, installing in /usr/local
teaiii at teaiii-Leopard-WS:~/R-3.2.2$ ./configure
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... missing
checking for working autoconf... missing
checking for working automake... missing
checking for working autoheader... missing
checking for gawk... no
checking for mawk... mawk
checking whether ln -s works... yes
checking for bison... bison -y
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... no
checking for gnutar... no
checking for tar... /bin/tar
checking for tex... /usr/bin/tex
checking for pdftex... /usr/bin/pdftex
checking for pdflatex... /usr/bin/pdflatex
checking for makeindex... /usr/bin/makeindex
checking for texi2any... no
configure: WARNING: you cannot build info or HTML versions of the R manuals
checking for texi2dvi... no
checking for kpsewhich... /usr/bin/kpsewhich
checking for latex inconsolata package... missing
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF
vignettes and package manuals will not be rendered optimally
checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /bin/gzip
checking for bzip2... /bin/bzip2
checking for firefox... /usr/bin/firefox
using default browser ... /usr/bin/firefox
checking for acroread... no
checking for acroread4... no
checking for xdg-open... /usr/bin/xdg-open
checking for notangle... false
checking for realpath... /usr/bin/realpath
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc needs -traditional... no
checking how to run the C preprocessor... gcc -E
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc accepts -fvisibility... yes
checking whether gfortran accepts -fvisibility... yes
checking for ANSI C header files... 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 minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking for Objective C++ compiler... trying some possibilities
checking whether g++ can compile ObjC++... no
checking whether can compile ObjC++... no
no working ObjC++ compiler found
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU Fortran 77 compiler... (cached) yes
checking whether gfortran accepts -g... (cached) yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries...
yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries...
yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries...
yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... yes
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/bin/ld) supports shared
libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... yes
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checking for rl_callback_read_char in -lreadline... no
checking for main in -lncurses... yes
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checking for history_truncate_file... yes
checking whether rl_completion_matches exists and is declared... yes
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checking for library containing opendir... none required
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checking sched.h usability... yes
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checking for string.h... (cached) yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking for GNU C library with version >= 2... yes
checking return type of signal handlers... void
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checking for pid_t... yes
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checking for type of socket length... socklen_t *
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checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for gcc option to accept ISO C99... -std=gnu99
checking for gcc -std=gnu99 option to accept ISO Standard C... (cached)
-std=gnu99
checking for inline... inline
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of double... 8
checking size of size_t... 8
checking size of long double... 16
checking whether we can compute C Make dependencies... yes, using $(CC) -MM
checking whether gcc -std=gnu99 supports -c -o FILE.lo... yes
checking for gcc -std=gnu99 option to support OpenMP... -fopenmp
checking how to get verbose linking output from gfortran... -v
checking for Fortran 77 libraries of gfortran... -L/usr/local/lib
-L/usr/lib/gcc/x86_64-linux-gnu/4.9
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../../lib -L/lib/x86_64-linux-gnu
-L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../.. -lgfortran -lm -lquadmath
checking how to get verbose linking output from gcc -std=gnu99... -v
checking for C libraries of gcc -std=gnu99... -L/usr/local/lib
-L/usr/lib/gcc/x86_64-linux-gnu/4.9
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../x86_64-linux-gnu
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../../../lib -L/lib/x86_64-linux-gnu
-L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib
-L/usr/lib/gcc/x86_64-linux-gnu/4.9/../../.. -lgcc_s
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no
extra underscore
checking whether gfortran appends underscores to external names... yes
checking whether gfortran appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether gfortran and gcc -std=gnu99 agree on int and double... yes
checking whether gfortran and gcc -std=gnu99 agree on double complex... yes
checking for gfortran option to support OpenMP... -fopenmp
checking whether g++ accepts -M for generating dependencies... yes
checking for g++ option to support OpenMP... -fopenmp
checking whether we can compute ObjC Make dependencies... no
checking whether C runtime needs -D__NO_MATH_INLINES... no
checking for xmkmf... no
checking whether g++ supports C++11 features by default... no
checking whether g++ supports C++11 features with -std=c++11... yes
checking for off_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether alloca is declared... yes
checking whether expm1 exists and is declared... yes
checking whether hypot exists and is declared... yes
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checking whether nearbyint exists and is declared... yes
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checking whether powl exists and is declared... yes
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checking whether va_copy exists and is declared... yes
checking for isblank... yes
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checking whether getgrgid exists and is declared... yes
checking whether getpwuid exists and is declared... yes
checking whether kill exists and is declared... yes
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checking whether getrlimit exists and is declared... yes
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checking whether getpriority exists and is declared... yes
checking whether chmod exists and is declared... yes
checking whether mkfifo exists and is declared... yes
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checking whether gettimeofday exists and is declared... yes
checking whether utimes exists and is declared... yes
checking whether times exists and is declared... yes
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checking whether localtime_r exists and is declared... yes
checking whether nl_langinfo exists and is declared... yes
checking whether access exists and is declared... yes
checking whether chdir exists and is declared... yes
checking whether execv exists and is declared... yes
checking whether ftruncate exists and is declared... yes
checking whether getcwd exists and is declared... yes
checking whether geteuid exists and is declared... yes
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checking whether link exists and is declared... yes
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checking whether sched_setaffinity exists and is declared... yes
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checking whether utime exists and is declared... yes
checking for clock_gettime in -lrt... yes
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checking whether glob exists and is declared... yes
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checking whether you have IEEE 754 floating-point arithmetic... yes
checking whether putenv("FOO") can unset an environment variable... yes
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checking for library containing connect... none required
checking for library containing gethostbyname... none required
checking for library containing xdr_string... none required
checking for __setfpucw... no
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checking for working isfinite... yes
checking for working log1p... yes
checking whether ftell works correctly on files opened for append... yes
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checking complex.h usability... yes
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checking for double complex... yes
checking whether C99 double complex is supported... yes
checking whether cabs exists and is declared... yes
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checking whether cexp exists and is declared... yes
checking whether clog exists and is declared... yes
checking whether csqrt exists and is declared... yes
checking whether cpow exists and is declared... yes
checking whether ccos exists and is declared... yes
checking whether csin exists and is declared... yes
checking whether ctan exists and is declared... yes
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checking whether casin exists and is declared... yes
checking whether catan exists and is declared... yes
checking whether ccosh exists and is declared... yes
checking whether csinh exists and is declared... yes
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checking whether 'struct tm' includes tm_zone... yes
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checking iconv.h usability... yes
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extern size_t iconv (iconv_t cd, char * *inbuf, size_t
*inbytesleft, char * *outbuf, size_t *outbytesleft);
checking wchar.h usability... yes
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checking for X... libraries , headers
checking for gethostbyname... yes
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checking for XtToolkitInitialize in -lXt... yes
using X11 ... yes
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checking for BSD networking... yes
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libcurl 7.38.0
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checking whether KERN_USRSTACK sysctl is supported... no
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checking whether we are using the GNU Fortran compiler... yes
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checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
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checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
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checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/bin/ld) supports shared
libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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checking for Fortran flag to compile .f95 files... none
checking for gfortran option to support OpenMP... -fopenmp
checking for recommended packages... yes
checking whether NLS is requested... yes
Configuring src/extra/intl directory
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checking whether we are using the GNU C Library 2 or newer... yes
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checking for simple visibility declarations... yes
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checking for getpagesize... yes
checking for working mmap... yes
checking whether integer division by zero raises SIGFPE... yes
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checking whether the inttypes.h PRIxNN macros are broken... no
checking whether imported symbols can be declared weak... yes
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checking for iconv declaration... (cached)
extern size_t iconv (iconv_t cd, char * *inbuf, size_t
*inbytesleft, char * *outbuf, size_t *outbytesleft);
checking for NL_LOCALE_NAME macro... yes
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checking version of bison... 3.0.2, ok
checking for long long int... yes
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R is now configured for x86_64-pc-linux-gnu
Source directory: .
Installation directory: /usr/local
C compiler: gcc -std=gnu99 -g -O2
Fortran 77 compiler: gfortran -g -O2
C++ compiler: g++ -g -O2
C++ 11 compiler: g++ -std=c++11 -g -O2
Fortran 90/95 compiler: gfortran -g -O2
Obj-C compiler:
Interfaces supported: X11
External libraries: readline, zlib, lzma, PCRE, curl
Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU
Options enabled: shared BLAS, R profiling
Capabilities skipped:
Options not enabled: memory profiling
Recommended packages: yes
configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF
vignettes and package manuals will not be rendered optimally
Thanks for looking at this; it's odd...
Tom
On Sun, Nov 8, 2015 at 5:16 PM, Dylan Beaudette <dylan.beaudette at gmail.com>
wrote:
> Hi Tom,
>
> I have encountered this in the past when compiling without X11
> support, thinking that I wouldn't need it on a headless server. Turns
> out you need X11 (or at least Cairo) for a working graphics device for
> PNG and JPG formats. Any chance that you can post your configure
> arguments or build information?
>
> Dylan
>
> On Sun, Nov 8, 2015 at 2:42 PM, Thomas Adams <tea3rd at gmail.com> wrote:
> > Edzer,
> >
> > That's the problem... dev.list() returns NULL -- I don't understand. I
> > built R from source and did not see any problems. Any thoughts what I
> > should look for in building R correctly? I have built R from source many
> > times in the past and I have never encountered this kind of problem.
> >
> > Thank you!
> >
> > Tom
> >
> > On Sun, Nov 8, 2015 at 2:49 PM, Edzer Pebesma <
> edzer.pebesma at uni-muenster.de
> >> wrote:
> >
> >> Me too.
> >>
> >> > dev.list()
> >> X11cairo
> >> 2
> >>
> >> What is your output of dev.list()? does plot(meuse.sr) work?
> >>
> >>
> >> On 08/11/15 21:45, Tim Appelhans wrote:
> >> > Hi Tom,
> >> > on Ubuntu 14.04 I can reproduce fig07.R without any problem
> >> > my sessionInfo()
> >> >
> >> > R version 3.2.2 (2015-08-14)
> >> > Platform: x86_64-pc-linux-gnu (64-bit)
> >> > Running under: Ubuntu 14.04.3 LTS
> >> >
> >> > locale:
> >> > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8
> >> > [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_DE.UTF-8
> >> > LC_MESSAGES=en_US.UTF-8
> >> > [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C
> >> > [10] LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8
> >> > LC_IDENTIFICATION=C
> >> >
> >> > attached base packages:
> >> > [1] stats graphics grDevices utils datasets methods base
> >> >
> >> > other attached packages:
> >> > [1] lattice_0.20-33 sp_1.2-1 gstat_1.1-0
> >> >
> >> > loaded via a namespace (and not attached):
> >> > [1] zoo_1.7-12 tools_3.2.2 xts_0.9-7 spacetime_1.1-4
> >> > grid_3.2.2 FNN_1.1
> >> > [7] intervals_0.15.1
> >> >
> >> > Cheers
> >> > Tim
> >> >
> >> > On 08.11.2015 21:37, Thomas Adams wrote:
> >> >> All:
> >> >>
> >> >> I was previously able to do the kind of thing I will illustrate below
> >> >> on an
> >> >> Intel based RedHat Linux system a few years ago. The simple task is
> to
> >> >> use
> >> >> GRASS GIS with R, reading both raster and vector data into R through
> >> >> rgrass7 (previously with spgrass6). Using spplot, display the raster
> and
> >> >> overlay the vector polygon (a river basin boundary) for reference.
> As I
> >> >> said, I have previously done this with success. However, now
> >> >> overlaying the
> >> >> vector polygon fails, both with my own data and with the following
> >> >> example:
> >> >> http://rspatial.r-forge.r-project.org/gallery/ -- see the example
> for
> >> >> fig07.RThe raster data draws, but I get the following...
> >> >>
> >> >>> spplot(zn, c("a", "b", "c", "d"),
> >> >> + names.attr = c("ordinary kriging", "universal kriging with dist to
> >> >> river",
> >> >> + "stratified kriging with flood freq", "inverse distance"),
> >> >> + as.table = TRUE, main = "log-zinc interpolation",
> >> >> + sp.layout = list(rv, scale, text1, text2))
> >> >>
> >> >> Warning messages:
> >> >> 1: In grid.Call.graphics(L_path, x$x, x$y, index, switch(x$rule,
> >> >> winding =
> >> >> 1L, :
> >> >> Path drawing not available for this device
> >> >> 2: In grid.Call.graphics(L_path, x$x, x$y, index, switch(x$rule,
> >> >> winding =
> >> >> 1L, :
> >> >> Path drawing not available for this device
> >> >> 3: In grid.Call.graphics(L_path, x$x, x$y, index, switch(x$rule,
> >> >> winding =
> >> >> 1L, :
> >> >> Path drawing not available for this device
> >> >> 4: In grid.Call.graphics(L_path, x$x, x$y, index, switch(x$rule,
> >> >> winding =
> >> >> 1L, :
> >> >> Path drawing not available for this device
> >> >>
> >> >>
> >> >> I am using Ubuntu 15.10 and R 3.2.2. I have searched the web for
> others
> >> >> having this problem to no avail...
> >> >>
> >> >> Thank you for your help.
> >> >>
> >> >> Best,
> >> >> Tom
> >> >>
> >> >>
> >> >> --
> >> >>
> >> >> [[alternative HTML version deleted]]
> >> >>
> >> >> _______________________________________________
> >> >> R-sig-Geo mailing list
> >> >> R-sig-Geo at r-project.org
> >> >> 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/
> >> Spatial Statistics Society http://www.spatialstatistics.info
> >>
> >>
> >> _______________________________________________
> >> R-sig-Geo mailing list
> >> R-sig-Geo at r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>
> >
> >
> >
> > --
> > Thomas E Adams, III
> > 2330 Jack Warner PKWY, #334
> > Tuscaloosa, AL 35401
> >
> > 1 (513) 739-9512 (cell)
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-sig-Geo mailing list
> > R-sig-Geo at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
--
Thomas E Adams, III
2330 Jack Warner PKWY, #334
Tuscaloosa, AL 35401
1 (513) 739-9512 (cell)
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