Error(s) in re-building vignettes:
  ...
--- re-building ‘New_rmcorr_paper_analyses_figures.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'http://cran.rstudio.com/src/contrib/sp_1.4-5.tar.gz'
Content type 'application/x-gzip' length 1049195 bytes (1.0 MB)
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downloaded 1.0 MB

trying URL 'http://cran.rstudio.com/src/contrib/raster_3.4-5.tar.gz'
Content type 'application/x-gzip' length 575921 bytes (562 KB)
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downloaded 562 KB

trying URL 'http://cran.rstudio.com/src/contrib/RcppArmadillo_0.10.2.2.0.tar.gz'
Content type 'application/x-gzip' length 1661194 bytes (1.6 MB)
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downloaded 1.6 MB

trying URL 'http://cran.rstudio.com/src/contrib/unmarked_1.0.1.tar.gz'
Content type 'application/x-gzip' length 2104102 bytes (2.0 MB)
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downloaded 2.0 MB

trying URL 'http://cran.rstudio.com/src/contrib/VGAM_1.1-5.tar.gz'
Content type 'application/x-gzip' length 1580498 bytes (1.5 MB)
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downloaded 1.5 MB

trying URL 'http://cran.rstudio.com/src/contrib/AICcmodavg_2.3-1.tar.gz'
Content type 'application/x-gzip' length 678217 bytes (662 KB)
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downloaded 662 KB

* installing *source* package ‘sp’ ...
** package ‘sp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c Rcentroid.c -o Rcentroid.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c gcdist.c -o gcdist.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c init.c -o init.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c pip.c -o pip.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c pip2.c -o pip2.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c sp_xports.c -o sp_xports.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c surfaceArea.c -o surfaceArea.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c zerodist.c -o zerodist.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -G -L/usr/local/lib -o sp.so Rcentroid.o gcdist.o init.o pip.o pip2.o sp_xports.o surfaceArea.o zerodist.o
installing to /tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/00LOCK-sp/00new/sp/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sp)
* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
** using staged installation
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... no
checking whether /home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 accepts -g... yes
checking how to run the C++ preprocessor... /home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -E
checking whether we are using the GNU C++ compiler... (cached) no
checking whether /home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 accepts -g... (cached) yes
checking whether we have a suitable tempdir... /tmp/RtmpZFay5q/working_dir
checking whether R CMD SHLIB can already compile programs using OpenMP... yes
checking LAPACK_LIBS... R-supplied partial LAPACK found
configure: WARNING: Some complex-valued LAPACK functions may not be available
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include -I../inst/include -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c RcppArmadillo.cpp -o RcppArmadillo.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include -I../inst/include -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c RcppExports.cpp -o RcppExports.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include -I../inst/include -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c fastLm.cpp -o fastLm.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -G -L/usr/local/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -L/home/ripley/R/cc/lib -lRlapack -L/home/ripley/R/cc/lib -lRblas -R/home/ripley/developerstudio12.6/lib -lfsu /home/ripley/developerstudio12.6/lib/compilers/libsunquad.a -lsunmath -lmtsk -lm
installing to /tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppArmadillo)
* installing *source* package ‘VGAM’ ...
** package ‘VGAM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c VGAM_init.c -o VGAM_init.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c caqo3.c -o caqo3.o
/home/ripley/developerstudio12.6/bin/f95  -PIC  -O -libmil -xtarget=native -xcache=generic -nofstore  -c ei.f -o ei.o
/home/ripley/developerstudio12.6/bin/f95  -PIC  -O -libmil -xtarget=native -xcache=generic -nofstore  -c fgam.f -o fgam.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c gautr.c -o gautr.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c lerchphi.c -o lerchphi.o
/home/ripley/developerstudio12.6/bin/f95  -PIC  -O -libmil -xtarget=native -xcache=generic -nofstore  -c lms.f -o lms.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c muxr3.c -o muxr3.o
/home/ripley/developerstudio12.6/bin/f95  -PIC  -O -libmil -xtarget=native -xcache=generic -nofstore  -c rgam.f -o rgam.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c rgam3.c -o rgam3.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c specfun3.c -o specfun3.o
/home/ripley/developerstudio12.6/bin/f95  -PIC  -O -libmil -xtarget=native -xcache=generic -nofstore  -c tyeepolygamma.f -o tyeepolygamma.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c tyeepolygamma3.c -o tyeepolygamma3.o
/home/ripley/developerstudio12.6/bin/f95  -PIC  -O -libmil -xtarget=native -xcache=generic -nofstore  -c vdigami.f -o vdigami.o
/home/ripley/developerstudio12.6/bin/f95  -PIC  -O -libmil -xtarget=native -xcache=generic -nofstore  -c veigen.f -o veigen.o
/home/ripley/developerstudio12.6/bin/f95  -PIC  -O -libmil -xtarget=native -xcache=generic -nofstore  -c vgam.f -o vgam.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c vgam3.c -o vgam3.o
/home/ripley/developerstudio12.6/bin/f95  -PIC  -O -libmil -xtarget=native -xcache=generic -nofstore  -c vlinpack1.f -o vlinpack1.o
/home/ripley/developerstudio12.6/bin/f95  -PIC  -O -libmil -xtarget=native -xcache=generic -nofstore  -c vlinpack2.f -o vlinpack2.o
/home/ripley/developerstudio12.6/bin/f95  -PIC  -O -libmil -xtarget=native -xcache=generic -nofstore  -c vlinpack3.f -o vlinpack3.o
/home/ripley/developerstudio12.6/bin/f95  -PIC  -O -libmil -xtarget=native -xcache=generic -nofstore  -c vmux.f -o vmux.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c vmux3.c -o vmux3.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c zeta3.c -o zeta3.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -G -L/usr/local/lib -o VGAM.so VGAM_init.o caqo3.o ei.o fgam.o gautr.o lerchphi.o lms.o muxr3.o rgam.o rgam3.o specfun3.o tyeepolygamma.o tyeepolygamma3.o vdigami.o veigen.o vgam.o vgam3.o vlinpack1.o vlinpack2.o vlinpack3.o vmux.o vmux3.o zeta3.o -R/home/ripley/developerstudio12.6/lib -lfsu /home/ripley/developerstudio12.6/lib/compilers/libsunquad.a -lsunmath -lmtsk -lm -lfsu /home/ripley/developerstudio12.6/lib/libfui.so.2
installing to /tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/00LOCK-VGAM/00new/VGAM/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (VGAM)
* installing *source* package ‘raster’ ...
** package ‘raster’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c RasterModule.cpp -o RasterModule.o
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_class_constructor.h", line 103: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 20:     Where: While instantiating "Rcpp::class_<SpPolyPart>::constructor(const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 20:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 100: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 20:     Where: While instantiating "Rcpp::class_<SpPolyPart>::constructor(const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 20:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_Field.h", line 76: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 21:     Where: While instantiating "Rcpp::class_<SpPolyPart>& Rcpp::class_<SpPolyPart>::field_readonly<std::vector<double>>(const char*, std::vector<double> SpPolyPart::*, const char*)".
"RasterModule.cpp", line 21:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_Field.h", line 76: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 23:     Where: While instantiating "Rcpp::class_<SpPolyPart>& Rcpp::class_<SpPolyPart>::field_readonly<SpExtent>(const char*, SpExtent SpPolyPart::*, const char*)".
"RasterModule.cpp", line 23:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 87: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 24:     Where: While instantiating "Rcpp::class_<SpPolyPart>& Rcpp::class_<SpPolyPart>::method<bool, std::vector<double>, std::vector<double>>(const char*, bool(SpPolyPart::*)(std::vector<double>,std::vector<double>), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 24:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 239: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 24:     Where: While instantiating "Rcpp::class_<SpPolyPart>& Rcpp::class_<SpPolyPart>::method<bool, std::vector<double>, std::vector<double>>(const char*, bool(SpPolyPart::*)(std::vector<double>,std::vector<double>), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 24:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 58: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 26:     Where: While instantiating "Rcpp::class_<SpPolyPart>& Rcpp::class_<SpPolyPart>::method<std::vector<double>, unsigned>(const char*, std::vector<double>(SpPolyPart::*)(unsigned), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 26:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 28: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 28:     Where: While instantiating "Rcpp::class_<SpPolyPart>& Rcpp::class_<SpPolyPart>::method<unsigned>(const char*, unsigned(SpPolyPart::*)(), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 28:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 28: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 29:     Where: While instantiating "Rcpp::class_<SpPolyPart>& Rcpp::class_<SpPolyPart>::method<bool>(const char*, bool(SpPolyPart::*)(), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 29:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_class_constructor.h", line 103: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 33:     Where: While instantiating "Rcpp::class_<SpPoly>::constructor(const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 33:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 100: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 33:     Where: While instantiating "Rcpp::class_<SpPoly>::constructor(const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 33:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_Field.h", line 76: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 34:     Where: While instantiating "Rcpp::class_<SpPoly>& Rcpp::class_<SpPoly>::field_readonly<SpExtent>(const char*, SpExtent SpPoly::*, const char*)".
"RasterModule.cpp", line 34:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 58: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 35:     Where: While instantiating "Rcpp::class_<SpPoly>& Rcpp::class_<SpPoly>::method<SpPolyPart, unsigned>(const char*, SpPolyPart(SpPoly::*)(unsigned), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 35:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 58: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 36:     Where: While instantiating "Rcpp::class_<SpPoly>& Rcpp::class_<SpPoly>::method<bool, SpPolyPart>(const char*, bool(SpPoly::*)(SpPolyPart), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 36:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 28: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 37:     Where: While instantiating "Rcpp::class_<SpPoly>& Rcpp::class_<SpPoly>::method<unsigned>(const char*, unsigned(SpPoly::*)(), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 37:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_Field.h", line 76: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 42:     Where: While instantiating "Rcpp::class_<SpPolygons>& Rcpp::class_<SpPolygons>::field_readonly<SpExtent>(const char*, SpExtent SpPolygons::*, const char*)".
"RasterModule.cpp", line 42:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_Field.h", line 68: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 43:     Where: While instantiating "Rcpp::class_<SpPolygons>& Rcpp::class_<SpPolygons>::field<std::vector<double>>(const char*, std::vector<double> SpPolygons::*, const char*)".
"RasterModule.cpp", line 43:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_Field.h", line 68: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 44:     Where: While instantiating "Rcpp::class_<SpPolygons>& Rcpp::class_<SpPolygons>::field<std::string>(const char*, std::string  SpPolygons::*, const char*)".
"RasterModule.cpp", line 44:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_class_constructor.h", line 103: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 45:     Where: While instantiating "Rcpp::class_<SpPolygons>::constructor(const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 45:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 100: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 45:     Where: While instantiating "Rcpp::class_<SpPolygons>::constructor(const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 45:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 58: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 46:     Where: While instantiating "Rcpp::class_<SpPolygons>& Rcpp::class_<SpPolygons>::method<SpPoly, unsigned>(const char*, SpPoly(SpPolygons::*)(unsigned), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 46:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 58: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 47:     Where: While instantiating "Rcpp::class_<SpPolygons>& Rcpp::class_<SpPolygons>::method<bool, SpPoly>(const char*, bool(SpPolygons::*)(SpPoly), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 47:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 28: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 48:     Where: While instantiating "Rcpp::class_<SpPolygons>& Rcpp::class_<SpPolygons>::method<unsigned>(const char*, unsigned(SpPolygons::*)(), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 48:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 58: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 50:     Where: While instantiating "Rcpp::class_<SpPolygons>& Rcpp::class_<SpPolygons>::method<double, unsigned>(const char*, double(SpPolygons::*)(unsigned), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 50:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 87: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 51:     Where: While instantiating "Rcpp::class_<SpPolygons>& Rcpp::class_<SpPolygons>::method<bool, unsigned, double>(const char*, bool(SpPolygons::*)(unsigned,double), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 51:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 174: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 53:     Where: While instantiating "Rcpp::class_<SpPolygons>& Rcpp::class_<SpPolygons>::method<std::vector<double>, unsigned, unsigned, std::vector<double>, std::vector<double>, double>(const char*, std::vector<double>(SpPolygons::*)(unsigned,unsigned,std::vector<double>,std::vector<double>,double), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 53:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 58: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 54:     Where: While instantiating "Rcpp::class_<SpPolygons>& Rcpp::class_<SpPolygons>::method<SpPolygons, std::vector<unsigned>>(const char*, SpPolygons(SpPolygons::*)(std::vector<unsigned>), const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 54:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_class_constructor.h", line 103: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 59:     Where: While instantiating "Rcpp::class_<SpExtent>::constructor(const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 59:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 100: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 59:     Where: While instantiating "Rcpp::class_<SpExtent>::constructor(const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 59:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_class_constructor.h", line 70: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 60:     Where: While instantiating "Rcpp::class_<SpExtent>& Rcpp::class_<SpExtent>::constructor<double, double, double, double>(const char*, bool(*)(SEXPREC**,int))".
"RasterModule.cpp", line 60:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_Add_Property.h", line 26: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 61:     Where: While instantiating "Rcpp::class_<SpExtent>& Rcpp::class_<SpExtent>::property<std::vector<double>>(const char*, std::vector<double>(SpExtent::*)(), const char*)".
"RasterModule.cpp", line 61:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_Add_Property.h", line 26: Warning: docstring hides Rcpp::class_Base::docstring.
"RasterModule.cpp", line 62:     Where: While instantiating "Rcpp::class_<SpExtent>& Rcpp::class_<SpExtent>::property<bool>(const char*, bool(SpExtent::*)(), const char*)".
"RasterModule.cpp", line 62:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 239: Warning: docstring hides Rcpp::class_Base::docstring.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 59:     Where: While instantiating "Rcpp::class_<SpPoly>::AddMethod(const char*, Rcpp::CppMethod<SpPoly>*, bool(*)(SEXPREC**,int), const char*)".
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 59:     Where: Instantiated from Rcpp::class_<SpPoly>& Rcpp::class_<SpPoly>::method<SpPolyPart, unsigned>(const char*, SpPolyPart(SpPoly::*)(unsigned), const char*, bool(*)(SEXPREC**,int)).
"RasterModule.cpp", line 35:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 239: Warning: docstring hides Rcpp::class_Base::docstring.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 59:     Where: While instantiating "Rcpp::class_<SpPolygons>::AddMethod(const char*, Rcpp::CppMethod<SpPolygons>*, bool(*)(SEXPREC**,int), const char*)".
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/Module_generated_method.h", line 59:     Where: Instantiated from Rcpp::class_<SpPolygons>& Rcpp::class_<SpPolygons>::method<SpPoly, unsigned>(const char*, SpPoly(SpPolygons::*)(unsigned), const char*, bool(*)(SEXPREC**,int)).
"RasterModule.cpp", line 46:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 288: Warning: name hides Rcpp::class_Base::name.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 276:     Where: While instantiating "Rcpp::class_<SpPolyPart>::method_names()".
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 276:     Where: Instantiated from Rcpp::class_<SpPolyPart>::class_(const char*, const char*).
"RasterModule.cpp", line 19:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 309: Warning: name hides Rcpp::class_Base::name.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 296:     Where: While instantiating "Rcpp::class_<SpPolyPart>::methods_arity()".
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 296:     Where: Instantiated from Rcpp::class_<SpPolyPart>::class_(const char*, const char*).
"RasterModule.cpp", line 19:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 333: Warning: name hides Rcpp::class_Base::name.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 320:     Where: While instantiating "Rcpp::class_<SpPolyPart>::methods_voidness()".
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 320:     Where: Instantiated from Rcpp::class_<SpPolyPart>::class_(const char*, const char*).
"RasterModule.cpp", line 19:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 288: Warning: name hides Rcpp::class_Base::name.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 276:     Where: While instantiating "Rcpp::class_<SpPoly>::method_names()".
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 276:     Where: Instantiated from Rcpp::class_<SpPoly>::class_(const char*, const char*).
"RasterModule.cpp", line 32:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 309: Warning: name hides Rcpp::class_Base::name.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 296:     Where: While instantiating "Rcpp::class_<SpPoly>::methods_arity()".
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 296:     Where: Instantiated from Rcpp::class_<SpPoly>::class_(const char*, const char*).
"RasterModule.cpp", line 32:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 333: Warning: name hides Rcpp::class_Base::name.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 320:     Where: While instantiating "Rcpp::class_<SpPoly>::methods_voidness()".
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 320:     Where: Instantiated from Rcpp::class_<SpPoly>::class_(const char*, const char*).
"RasterModule.cpp", line 32:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 288: Warning: name hides Rcpp::class_Base::name.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 276:     Where: While instantiating "Rcpp::class_<SpPolygons>::method_names()".
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 276:     Where: Instantiated from Rcpp::class_<SpPolygons>::class_(const char*, const char*).
"RasterModule.cpp", line 40:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 309: Warning: name hides Rcpp::class_Base::name.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 296:     Where: While instantiating "Rcpp::class_<SpPolygons>::methods_arity()".
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 296:     Where: Instantiated from Rcpp::class_<SpPolygons>::class_(const char*, const char*).
"RasterModule.cpp", line 40:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 333: Warning: name hides Rcpp::class_Base::name.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 320:     Where: While instantiating "Rcpp::class_<SpPolygons>::methods_voidness()".
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 320:     Where: Instantiated from Rcpp::class_<SpPolygons>::class_(const char*, const char*).
"RasterModule.cpp", line 40:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 288: Warning: name hides Rcpp::class_Base::name.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 276:     Where: While instantiating "Rcpp::class_<SpExtent>::method_names()".
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 276:     Where: Instantiated from Rcpp::class_<SpExtent>::class_(const char*, const char*).
"RasterModule.cpp", line 58:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 309: Warning: name hides Rcpp::class_Base::name.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 296:     Where: While instantiating "Rcpp::class_<SpExtent>::methods_arity()".
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 296:     Where: Instantiated from Rcpp::class_<SpExtent>::class_(const char*, const char*).
"RasterModule.cpp", line 58:     Where: Instantiated from non-template code.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 333: Warning: name hides Rcpp::class_Base::name.
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 320:     Where: While instantiating "Rcpp::class_<SpExtent>::methods_voidness()".
"/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include/Rcpp/module/class.h", line 320:     Where: Instantiated from Rcpp::class_<SpExtent>::class_(const char*, const char*).
"RasterModule.cpp", line 58:     Where: Instantiated from non-template code.
46 Warning(s) detected.
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c RcppExports.cpp -o RcppExports.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c aggregate.cpp -o aggregate.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c area.cpp -o area.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c bilinear.cpp -o bilinear.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c broom.cpp -o broom.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c cellRowCol.cpp -o cellRowCol.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c clamp.cpp -o clamp.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c distance.cpp -o distance.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c edge.cpp -o edge.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c focal_fun.cpp -o focal_fun.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c focal_get.cpp -o focal_get.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c focal_sum.cpp -o focal_sum.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c geodesic.c -o geodesic.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c getPolygons.cpp -o getPolygons.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c layerize.cpp -o layerize.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c memory.cpp -o memory.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c modal.cpp -o modal.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c ppmin.cpp -o ppmin.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c raster_aggregate.cpp -o raster_aggregate.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c raster_distance.cpp -o raster_distance.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c rasterize.cpp -o rasterize.o
"rasterize.cpp", line 53: Warning: extent hides SpPolygons::extent.
1 Warning(s) detected.
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c reclass.cpp -o reclass.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c terrain.cpp -o terrain.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c util.cpp -o util.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -I"/home/ripley/R/cc/include" -DNDEBUG  -I'/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/Rcpp/include' -I/usr/local/include  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c xyCell.cpp -o xyCell.o
/home/ripley/developerstudio12.6/bin/CC -std=c++11 -library=stdcpp,CrunG3 -G -L/usr/local/lib -o raster.so RasterModule.o RcppExports.o aggregate.o area.o bilinear.o broom.o cellRowCol.o clamp.o distance.o edge.o focal_fun.o focal_get.o focal_sum.o geodesic.o getPolygons.o layerize.o memory.o modal.o ppmin.o raster_aggregate.o raster_distance.o rasterize.o reclass.o terrain.o util.o xyCell.o
installing to /tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/00LOCK-raster/00new/raster/libs
** R
** inst
** byte-compile and prepare package for lazy loading
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 ‘brick’ with signature ‘x="SpatRaster"’: no definition for class “SpatRaster”
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 ‘ncol’ from package ‘base’ in package ‘raster’
in method for ‘extent’ with signature ‘x="bbox"’: no definition for class “bbox”
in method for ‘extent’ with signature ‘x="sf"’: no definition for class “sf”
in method for ‘extract’ with signature ‘x="Raster",y="sf"’: no definition for class “sf”
in method for ‘mask’ with signature ‘x="Raster",mask="sf"’: no definition for class “sf”
in method for ‘raster’ with signature ‘x="sf"’: no definition for class “sf”
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”
in method for ‘raster’ with signature ‘x="SpatRaster"’: no definition for class “SpatRaster”
in method for ‘rasterize’ with signature ‘x="sf",y="Raster"’: no definition for class “sf”
Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘raster’
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘raster’
in method for ‘setValues’ with signature ‘x="RasterLayerSparse"’: no definition for class “RasterLayerSparse”
in method for ‘spplot’ with signature ‘obj="SpatRaster"’: no definition for class “SpatRaster”
in method for ‘spplot’ with signature ‘obj="SpatVector"’: no definition for class “SpatVector”
in method for ‘stack’ with signature ‘x="kasc"’: no definition for class “kasc”
in method for ‘stack’ with signature ‘x="SpatRaster"’: no definition for class “SpatRaster”
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: Module(module, mustStart = TRUE, where = env)
 2: doTryCatch(return(expr), name, parentenv, handler)
 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 4: tryCatchList(expr, classes, parentenv, handlers)
 5: tryCatch(Module(module, mustStart = TRUE, where = env), error = function(e) e)
 6: loadModule(module = "spmod", what = TRUE, env = ns, loadNow = TRUE)
 7: (function (ns) loadModule(module = "spmod", what = TRUE, env = ns, loadNow = TRUE))(<environment>)
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch((function (ns) loadModule(module = "spmod", what = TRUE, env = ns, loadNow = TRUE))(<environment>),     error = function(e) e)
12: eval(substitute(tryCatch(FUN(WHERE), error = function(e) e),     list(FUN = f, WHERE = where)), where)
13: eval(substitute(tryCatch(FUN(WHERE), error = function(e) e),     list(FUN = f, WHERE = where)), where)
14: .doLoadActions(where, attach)
15: methods::cacheMetaData(ns, TRUE, ns)
16: loadNamespace(package, lib.loc)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
21: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)
22: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
23: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,     character.only = TRUE, logical.return = TRUE))
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
26: tryCatchList(expr, classes, parentenv, handlers)
27: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
28: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,     character.only = TRUE, logical.return = TRUE)))
29: tools:::.test_load_package("raster", "/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/00LOCK-raster/00new")
An irrecoverable exception occurred. R is aborting now ...
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: Module(module, mustStart = TRUE, where = env)
 2: doTryCatch(return(expr), name, parentenv, handler)
 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 4: tryCatchList(expr, classes, parentenv, handlers)
 5: tryCatch(Module(module, mustStart = TRUE, where = env), error = function(e) e)
 6: loadModule(module = "spmod", what = TRUE, env = ns, loadNow = TRUE)
 7: (function (ns) loadModule(module = "spmod", what = TRUE, env = ns, loadNow = TRUE))(<environment>)
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch((function (ns) loadModule(module = "spmod", what = TRUE, env = ns, loadNow = TRUE))(<environment>),     error = function(e) e)
12: eval(substitute(tryCatch(FUN(WHERE), error = function(e) e),     list(FUN = f, WHERE = where)), where)
13: eval(substitute(tryCatch(FUN(WHERE), error = function(e) e),     list(FUN = f, WHERE = where)), where)
14: .doLoadActions(where, attach)
15: methods::cacheMetaData(ns, TRUE, ns)
16: loadNamespace(package, lib.loc)
17: doTryCatch(return(expr), name, parentenv, handler)
18: tryCatchOne(expr, names, parentenv, handlers[[1L]])
19: tryCatchList(expr, classes, parentenv, handlers)
20: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
21: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE)
22: withCallingHandlers(expr, packageStartupMessage = function(c) tryInvokeRestart("muffleMessage"))
23: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,     character.only = TRUE, logical.return = TRUE))
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
26: tryCatchList(expr, classes, parentenv, handlers)
27: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
28: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,     character.only = TRUE, logical.return = TRUE)))
29: tools:::.test_load_package("raster", "/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6")
An irrecoverable exception occurred. R is aborting now ...
** testing if installed package keeps a record of temporary installation path
Warning in file(con, "rb") :
  cannot open file '/tmp/RtmpZFay5q/working_dir/RtmpoFaam1/file6a604d702b6c': No such file or directory
Error in file(con, "rb") : cannot open the connection
* removing ‘/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/raster’
ERROR: dependency ‘raster’ is not available for package ‘unmarked’
* removing ‘/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/unmarked’
ERROR: dependency ‘unmarked’ is not available for package ‘AICcmodavg’
* removing ‘/tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/AICcmodavg’

The downloaded source packages are in
	'/tmp/RtmpZFay5q/working_dir/RtmpN_aW.v/downloaded_packages'
trying URL 'http://cran.rstudio.com/src/contrib/dichromat_2.0-0.tar.gz'
Content type 'application/x-gzip' length 84320 bytes (82 KB)
==================================================
downloaded 82 KB

trying URL 'http://cran.rstudio.com/src/contrib/mapproj_1.2.7.tar.gz'
Content type 'application/x-gzip' length 25429 bytes (24 KB)
==================================================
downloaded 24 KB

trying URL 'http://cran.rstudio.com/src/contrib/maps_3.3.0.tar.gz'
Content type 'application/x-gzip' length 2493744 bytes (2.4 MB)
==================================================
downloaded 2.4 MB

trying URL 'http://cran.rstudio.com/src/contrib/pals_1.6.tar.gz'
Content type 'application/x-gzip' length 2453027 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

* installing *source* package ‘dichromat’ ...
** package ‘dichromat’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dichromat)
* installing *source* package ‘maps’ ...
** package ‘maps’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gawk... no
checking for mawk... no
checking for nawk... nawk
configure: creating ./config.status
config.status: creating src/Makefile
** libs
** arch - 
make -f "/home/ripley/R/cc/etc/Makeconf" -f Makefile init.o mapclip.o mapget.o smooth.o thin.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c init.c -o init.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c mapclip.c -o mapclip.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c mapget.c -o mapget.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c smooth.c -o smooth.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c thin.c -o thin.o
"/home/ripley/R/cc/bin/R" CMD SHLIB -o maps.so init.o mapclip.o mapget.o smooth.o thin.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -G -L/usr/local/lib -o maps.so init.o mapclip.o mapget.o smooth.o thin.o
make -f "/home/ripley/R/cc/etc/Makeconf" -f Makefile Gmake
/home/ripley/developerstudio12.6/bin/cc -xc99 -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -I/usr/local/include -L/usr/local/lib -o Gmake Gmake.c 
make -f "/home/ripley/R/cc/etc/Makeconf" -f Makefile Lmake
/home/ripley/developerstudio12.6/bin/cc -xc99 -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -I/usr/local/include -L/usr/local/lib -o Lmake Lmake.c 
make -f "/home/ripley/R/cc/etc/Makeconf" -f Makefile world2.line
Converting world to world2
nawk -f ./convert.awk < world.line > world2.line
Creating legacy world2 database
nawk -f ./legacy_convert.awk < legacy_world.line > legacy_world2.line
make -f "/home/ripley/R/cc/etc/Makeconf" -f Makefile county.L state.L usa.L nz.L world.L world2.L italy.L france.L state.vbm.L  state.carto.L legacy_world.L legacy_world2.L lakes.L
./Lmake 0 s b county.line county.linestats ../inst/mapdata/county.L
./Lmake 0 s b state.line state.linestats ../inst/mapdata/state.L
./Lmake 0 s b usa.line usa.linestats ../inst/mapdata/usa.L
./Lmake 0 s b nz.line nz.linestats ../inst/mapdata/nz.L
./Lmake 0 s b world.line world.linestats ../inst/mapdata/world.L
./Lmake 0 s b world2.line world2.linestats ../inst/mapdata/world2.L
./Lmake 0 s b italy.line italy.linestats ../inst/mapdata/italy.L
./Lmake 0 s b france.line france.linestats ../inst/mapdata/france.L
./Lmake 0 p b state.vbm.line state.vbm.linestats ../inst/mapdata/state.vbm.L
./Lmake 0 p b state.carto.line state.carto.linestats ../inst/mapdata/state.carto.L
./Lmake 0 s b legacy_world.line legacy_world.linestats ../inst/mapdata/legacy_world.L
./Lmake 0 s b legacy_world2.line legacy_world2.linestats ../inst/mapdata/legacy_world2.L
./Lmake 0 s b lakes.line lakes.linestats ../inst/mapdata/lakes.L
make -f "/home/ripley/R/cc/etc/Makeconf" -f Makefile county.G state.G usa.G nz.G world.G world2.G italy.G france.G state.vbm.G  state.carto.G legacy_world.G legacy_world2.G lakes.G
./Gmake b county.gon county.gonstats ../inst/mapdata/county.G ../inst/mapdata/county.L
./Gmake b state.gon state.gonstats ../inst/mapdata/state.G ../inst/mapdata/state.L
./Gmake b usa.gon usa.gonstats ../inst/mapdata/usa.G ../inst/mapdata/usa.L
./Gmake b nz.gon nz.gonstats ../inst/mapdata/nz.G ../inst/mapdata/nz.L
./Gmake b world.gon world.gonstats ../inst/mapdata/world.G ../inst/mapdata/world.L
./Gmake b world2.gon world2.gonstats ../inst/mapdata/world2.G ../inst/mapdata/world2.L
./Gmake b italy.gon italy.gonstats ../inst/mapdata/italy.G ../inst/mapdata/italy.L
./Gmake b france.gon france.gonstats ../inst/mapdata/france.G ../inst/mapdata/france.L
./Gmake b state.vbm.gon state.vbm.gonstats ../inst/mapdata/state.vbm.G ../inst/mapdata/state.vbm.L
./Gmake b state.carto.gon state.carto.gonstats ../inst/mapdata/state.carto.G ../inst/mapdata/state.carto.L
./Gmake b legacy_world.gon legacy_world.gonstats ../inst/mapdata/legacy_world.G ../inst/mapdata/legacy_world.L
./Gmake b legacy_world2.gon legacy_world2.gonstats ../inst/mapdata/legacy_world2.G ../inst/mapdata/legacy_world2.L
./Gmake b lakes.gon lakes.gonstats ../inst/mapdata/lakes.G ../inst/mapdata/lakes.L
make -f "/home/ripley/R/cc/etc/Makeconf" -f Makefile county.N state.N usa.N nz.N world.N world2.N italy.N france.N state.vbm.N  state.carto.N legacy_world.N legacy_world2.N lakes.N
installing to /tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/00LOCK-maps/00new/maps/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maps)
* installing *source* package ‘mapproj’ ...
** package ‘mapproj’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c aitoff.c -o aitoff.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c albers.c -o albers.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c azequalarea.c -o azequalarea.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c azequidist.c -o azequidist.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c bicentric.c -o bicentric.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c bonne.c -o bonne.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c ccubrt.c -o ccubrt.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c complex.c -o complex.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c conic.c -o conic.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c cubrt.c -o cubrt.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c cuts.c -o cuts.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c cylequalarea.c -o cylequalarea.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c cylindrical.c -o cylindrical.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c eisenlohr.c -o eisenlohr.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c elco2.c -o elco2.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c elliptic.c -o elliptic.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c fisheye.c -o fisheye.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c gall.c -o gall.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c gilbert.c -o gilbert.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c guyou.c -o guyou.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c harrison.c -o harrison.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c hex.c -o hex.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c homing.c -o homing.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c init.c -o init.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c lagrange.c -o lagrange.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c lambert.c -o lambert.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c laue.c -o laue.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c lune.c -o lune.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c mapproject.c -o mapproject.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c mercator.c -o mercator.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c mollweide.c -o mollweide.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c newyorker.c -o newyorker.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c orthographic.c -o orthographic.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c perspective.c -o perspective.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c polyconic.c -o polyconic.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c rectangular.c -o rectangular.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c simpleconic.c -o simpleconic.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c sinusoidal.c -o sinusoidal.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c tetra.c -o tetra.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c trapezoidal.c -o trapezoidal.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c twocirc.c -o twocirc.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -I"/home/ripley/R/cc/include" -DNDEBUG   -I/usr/local/include  -KPIC  -O -xlibmieee -xlibmil -xtarget=native -xcache=generic -nofstore  -c zcoord.c -o zcoord.o
/home/ripley/developerstudio12.6/bin/cc -xc99 -G -L/usr/local/lib -o mapproj.so aitoff.o albers.o azequalarea.o azequidist.o bicentric.o bonne.o ccubrt.o complex.o conic.o cubrt.o cuts.o cylequalarea.o cylindrical.o eisenlohr.o elco2.o elliptic.o fisheye.o gall.o gilbert.o guyou.o harrison.o hex.o homing.o init.o lagrange.o lambert.o laue.o lune.o mapproject.o mercator.o mollweide.o newyorker.o orthographic.o perspective.o polyconic.o rectangular.o simpleconic.o sinusoidal.o tetra.o trapezoidal.o twocirc.o zcoord.o
installing to /tmp/RtmpZFay5q/RLIBS_21cb2dc72fc6/00LOCK-mapproj/00new/mapproj/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (mapproj)
* installing *source* package ‘pals’ ...
** package ‘pals’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pals)

The downloaded source packages are in
	'/tmp/RtmpZFay5q/working_dir/RtmpN_aW.v/downloaded_packages'
Warning in rmcorr(participant = Participant, measure1 = Age, measure2 = Volume,  :
  'Participant' coerced into a factor
Warning in rmcorr(participant = sub, measure1 = rt, measure2 = acc, dataset = gilden2010) :
  'sub' coerced into a factor
Quitting from lines 640-716 (New_rmcorr_paper_analyses_figures.Rmd) 
Error: processing vignette 'New_rmcorr_paper_analyses_figures.Rmd' failed with diagnostics:
could not find function "aictab"
--- failed re-building ‘New_rmcorr_paper_analyses_figures.Rmd’

SUMMARY: processing the following file failed:
  ‘New_rmcorr_paper_analyses_figures.Rmd’

Error: Vignette re-building failed.
Execution halted