processing_script.r.Rout

R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

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> options("repos"="http://cran.at.r-project.org/")
> tryCatch(find.package("rgdal"), error=function(e) install.packages("rgdal", dependencies=TRUE))
Installing package into ‘/home/office/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
Warning message:
package ‘rgdal’ is not available (for R version 3.2.3) 
> tryCatch(find.package("raster"), error=function(e) install.packages("raster", dependencies=TRUE))
Installing package into ‘/home/office/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
Warning: dependency ‘rgdal’ is not available
also installing the dependencies ‘latticeExtra’, ‘sp’, ‘rgeos’, ‘ncdf4’, ‘rasterVis’

trying URL 'http://cran.at.r-project.org/src/contrib/latticeExtra_0.6-28.tar.gz'
Content type 'application/x-gzip' length 1294369 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'http://cran.at.r-project.org/src/contrib/sp_1.2-5.tar.gz'
Content type 'application/x-gzip' length 1134121 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'http://cran.at.r-project.org/src/contrib/rgeos_0.3-23.tar.gz'
Content type 'application/x-gzip' length 257486 bytes (251 KB)
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downloaded 251 KB

trying URL 'http://cran.at.r-project.org/src/contrib/ncdf4_1.16.tar.gz'
Content type 'application/x-gzip' length 121420 bytes (118 KB)
==================================================
downloaded 118 KB

trying URL 'http://cran.at.r-project.org/src/contrib/rasterVis_0.41.tar.gz'
Content type 'application/x-gzip' length 40749 bytes (39 KB)
==================================================
downloaded 39 KB

trying URL 'http://cran.at.r-project.org/src/contrib/raster_2.5-8.tar.gz'
Content type 'application/x-gzip' length 1092017 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

* installing *source* package ‘latticeExtra’ ...
** package ‘latticeExtra’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (latticeExtra)
* installing *source* package ‘sp’ ...
** package ‘sp’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rcentroid.c -o Rcentroid.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gcdist.c -o gcdist.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pip.c -o pip.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pip2.c -o pip2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sp_xports.c -o sp_xports.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c surfaceArea.c -o surfaceArea.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zerodist.c -o zerodist.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o sp.so Rcentroid.o gcdist.o init.o pip.o pip2.o sp_xports.o surfaceArea.o zerodist.o -L/usr/lib/R/lib -lR
installing to /home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sp)
* installing *source* package ‘ncdf4’ ...
** package ‘ncdf4’ successfully unpacked and MD5 sums checked
configure.ac: starting
checking for nc-config... yes
Using nc-config: nc-config
Output of nc-config --all:

This netCDF 4.4.0 has been built with the following features: 

  --cc        -> /usr/bin/x86_64-linux-gnu-gcc
  --cflags    -> -I/usr/include -I/usr/include/hdf5/serial
  --libs      -> -L/usr/lib -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -lhdf5_hl -lhdf5 -lpthread -lsz -lz -ldl -lm -lcurl

  --has-c++   -> no
  --cxx       -> 
  --has-c++4  -> no
  --cxx4      -> 

  --fc        -> 
  --fflags    -> 
  --flibs     -> 
  --has-f90   -> no

  --has-dap   -> yes
  --has-nc2   -> yes
  --has-nc4   -> yes
  --has-hdf5  -> yes
  --has-hdf4  -> no
  --has-pnetcdf-> no
  --has-szlib -> no

  --prefix    -> /usr
  --includedir-> /usr/include
  --version   -> netCDF 4.4.0

---
netcdf.m4: about to set rpath, here is source string: >-L/usr/lib -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -lhdf5_hl -lhdf5 -lpthread -lsz -lz -ldl -lm -lcurl<
netcdf.m4: final rpath:   -Wl,-rpath,/usr/lib -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial
Netcdf library version: netCDF 4.4.0
Netcdf library has version 4 interface present: yes
Netcdf library was compiled with C compiler: /usr/bin/x86_64-linux-gnu-gcc
configure: creating ./config.status
config.status: creating src/Makevars
 
**********************  Results of ncdf4 package configure *******************
 
netCDF v4 CPP flags      = -I/usr/include -I/usr/include/hdf5/serial
netCDF v4 LD flags       =   -Wl,-rpath,/usr/lib -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial -L/usr/lib -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -lhdf5_hl -lhdf5 -lpthread -lsz -lz -ldl -lm -lcurl 
netCDF v4 runtime path   =   -Wl,-rpath,/usr/lib -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial
 
netCDF C compiler used   = /usr/bin/x86_64-linux-gnu-gcc
R      C compiler used   = gcc -std=gnu99 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
 
******************************************************************************
 
netcdf cc arg1: /usr/bin/x86_64-linux-gnu-gcc  R cc arg1: gcc R_IS_GCC: 1 R_IS_CLANG: 0 NETCDF_IS_GCC: 1 NETCDF_IS_CLANG: 0  emit_warning: 0
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include -I/usr/include/hdf5/serial     -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ncdf.c -o ncdf.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ncdf4.so ncdf.o -Wl,-rpath,/usr/lib -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial -L/usr/lib -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -lhdf5_hl -lhdf5 -lpthread -lsz -lz -ldl -lm -lcurl -L/usr/lib/R/lib -lR
installing to /home/office/R/x86_64-pc-linux-gnu-library/3.2/ncdf4/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (ncdf4)
* installing *source* package ‘rgeos’ ...
** package ‘rgeos’ successfully unpacked and MD5 sums checked
configure: CC: gcc -std=gnu99
configure: CXX: g++
configure: rgeos: 0.3-23
checking for /usr/bin/svnversion... yes
configure: svn revision: 546
checking for geos-config... /usr/bin/geos-config
checking geos-config usability... yes
configure: GEOS version: 3.5.0
checking geos version at least 3.2.0... yes
checking geos-config clibs... yes
checking for gcc... gcc -std=gnu99
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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
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 geos_c.h usability... yes
checking geos_c.h presence... yes
checking for geos_c.h... yes
checking geos: linking with libgeos_c... yes
configure: PKG_CPPFLAGS:  -I/usr/include
configure: PKG_LIBS:  -L/usr/lib/x86_64-linux-gnu -lgeos-3.5.0 -L/usr/lib/x86_64-linux-gnu -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dummy.cc -o dummy.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c local_stubs.c -o local_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos.c -o rgeos.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_R2geos.c -o rgeos_R2geos.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_R2geosMP.c -o rgeos_R2geosMP.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_bbox.c -o rgeos_bbox.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_buffer.c -o rgeos_buffer.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_coord.c -o rgeos_coord.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_geos2R.c -o rgeos_geos2R.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_linearref.c -o rgeos_linearref.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_misc.c -o rgeos_misc.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_poly2nb.c -o rgeos_poly2nb.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_predicate_binary.c -o rgeos_predicate_binary.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_predicate_unary.c -o rgeos_predicate_unary.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_topology.c -o rgeos_topology.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_topology_binary.c -o rgeos_topology_binary.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_validate.c -o rgeos_validate.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/include  -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/sp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rgeos_wkt.c -o rgeos_wkt.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o rgeos.so dummy.o init.o local_stubs.o rgeos.o rgeos_R2geos.o rgeos_R2geosMP.o rgeos_bbox.o rgeos_buffer.o rgeos_coord.o rgeos_geos2R.o rgeos_linearref.o rgeos_misc.o rgeos_poly2nb.o rgeos_predicate_binary.o rgeos_predicate_unary.o rgeos_topology.o rgeos_topology_binary.o rgeos_validate.o rgeos_wkt.o -L/usr/lib/x86_64-linux-gnu -lgeos-3.5.0 -L/usr/lib/x86_64-linux-gnu -lgeos_c -L/usr/lib/R/lib -lR
installing to /home/office/R/x86_64-pc-linux-gnu-library/3.2/rgeos/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rgeos)
* installing *source* package ‘raster’ ...
** package ‘raster’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c aggregate.c -o aggregate.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c aggregate_get.c -o aggregate_get.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bilinear.cpp -o bilinear.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c broom.c -o broom.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cellRowCol.cpp -o cellRowCol.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c clamp.c -o clamp.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c direction.c -o direction.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dist_util.c -o dist_util.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c distance.c -o distance.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c edge.c -o edge.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c focal_fun.c -o focal_fun.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c focal_get.c -o focal_get.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c focal_sum.c -o focal_sum.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c geodesic.c -o geodesic.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c geolib.c -o geolib.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c getPolygons.cpp -o getPolygons.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c intersect.c -o intersect.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c layerize.c -o layerize.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c modal.cpp -o modal.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pointinpoly.c -o pointinpoly.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ppmin.cpp -o ppmin.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c reclass.c -o reclass.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c solar.c -o solar.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c terrain.c -o terrain.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c util.c -o util.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c wirth.c -o wirth.o
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/office/R/x86_64-pc-linux-gnu-library/3.2/Rcpp/include"   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xyCell.cpp -o xyCell.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o raster.so RcppExports.o aggregate.o aggregate_get.o bilinear.o broom.o cellRowCol.o clamp.o direction.o dist_util.o distance.o edge.o focal_fun.o focal_get.o focal_sum.o geodesic.o geolib.o getPolygons.o intersect.o layerize.o modal.o pointinpoly.o ppmin.o reclass.o solar.o terrain.o util.o wirth.o xyCell.o -L/usr/lib/R/lib -lR
installing to /home/office/R/x86_64-pc-linux-gnu-library/3.2/raster/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘aggregate’ from package ‘stats’ in package ‘raster’
Creating a generic function for ‘as.array’ from package ‘base’ in package ‘raster’
Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘raster’
Creating a generic function for ‘as.vector’ from package ‘base’ in package ‘raster’
in method for ‘brick’ with signature ‘x="big.matrix"’: no definition for class “big.matrix”
in method for ‘brick’ with signature ‘x="kasc"’: no definition for class “kasc”
in method for ‘brick’ with signature ‘x="grf"’: no definition for class “grf”
in method for ‘coerce’ with signature ‘"STFDF","RasterBrick"’: no definition for class “STFDF”
in method for ‘coerce’ with signature ‘"STSDF","RasterBrick"’: no definition for class “STSDF”
in method for ‘coerce’ with signature ‘"asc","RasterLayer"’: no definition for class “asc”
in method for ‘coerce’ with signature ‘"RasterLayer","asc"’: no definition for class “asc”
in method for ‘coerce’ with signature ‘"kasc","RasterBrick"’: no definition for class “kasc”
in method for ‘coerce’ with signature ‘"kasc","RasterStack"’: no definition for class “kasc”
in method for ‘coerce’ with signature ‘"kde","RasterLayer"’: no definition for class “kde”
in method for ‘coerce’ with signature ‘"grf","RasterBrick"’: no definition for class “grf”
in method for ‘coerce’ with signature ‘"grf","RasterLayer"’: no definition for class “grf”
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘raster’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘raster’
Creating a generic function for ‘hist’ from package ‘graphics’ in package ‘raster’
Creating a generic function for ‘as.list’ from package ‘base’ in package ‘raster’
Creating a generic function for ‘mean’ from package ‘base’ in package ‘raster’
Creating a generic function for ‘labels’ from package ‘base’ in package ‘raster’
Creating a generic function for ‘lines’ from package ‘graphics’ in package ‘raster’
Creating a generic function for ‘print’ from package ‘base’ in package ‘raster’
Creating a generic function for ‘quantile’ from package ‘stats’ in package ‘raster’
in method for ‘raster’ with signature ‘x="big.matrix"’: no definition for class “big.matrix”
in method for ‘raster’ with signature ‘x="kasc"’: no definition for class “kasc”
in method for ‘raster’ with signature ‘x="asc"’: no definition for class “asc”
in method for ‘raster’ with signature ‘x="kde"’: no definition for class “kde”
in method for ‘raster’ with signature ‘x="grf"’: no definition for class “grf”
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘raster’
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘raster’
Creating a generic function for ‘scale’ from package ‘base’ in package ‘raster’
in method for ‘stack’ with signature ‘x="kasc"’: no definition for class “kasc”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (raster)
* installing *source* package ‘rasterVis’ ...
** package ‘rasterVis’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rasterVis)

The downloaded source packages are in
	‘/tmp/Rtmp4pVyOj/downloaded_packages’
> library("raster")
Loading required package: sp
> library("rgdal")
Error in library("rgdal") : there is no package called ‘rgdal’
Execution halted