SDMTools - Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises - check results
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SDMTools

About SDMTools
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Package R docs

Version: 1.1-221
Result: OK
Check time: 2018-01-26 16:22
* using log directory ''
* using R Under development (unstable) (2018-01-26 r74168)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'SDMTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SDMTools' version '1.1-221'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialized R objects in the sources ... OK
* checking whether package 'SDMTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
'raster' 'sp'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
COGravity: no visible global function definition for 'sd'
ClassStat: no visible global function definition for 'na.omit'
ClassStat: no visible global function definition for 'sd'
ConnCompLabel: no visible global function definition for 'setValues'
ImageDiff: no visible global function definition for 'terrain.colors'
ImageDiff: no visible global function definition for 'image'
PatchStat: no visible global function definition for 'na.omit'
Scalebar: no visible global function definition for 'rect'
Scalebar: no visible global function definition for 'segments'
Scalebar: no visible global function definition for 'text'
SigDiff: no visible global function definition for 'pnorm'
SigDiff: no visible global function definition for 'setValues'
ZonalStat: no visible global function definition for 'na.omit'
ZonalStat: no visible global function definition for 'quantile'
asc.from.raster: no visible global function definition for 'getValues'
asc2dataframe: no visible global function definition for 'na.omit'
aspect: no visible global function definition for 'setValues'
compare.matrix: no visible global function definition for 'aggregate'
compare.matrix: no visible global function definition for 'image'
compare.matrix: no visible global function definition for 'heat.colors'
compare.matrix: no visible global function definition for 'contour'
grid.area: no visible global function definition for 'setValues'
grid.perimeter: no visible global function definition for 'setValues'
image.asc: no visible global function definition for 'gray'
image.asc: no visible global function definition for 'image'
image.asc: no visible global function definition for 'rainbow'
lcmw: no visible global function definition for 'na.omit'
lcmw: no visible global function definition for 'setValues'
legend.gradient: no visible global function definition for
'heat.colors'
legend.gradient: no visible global function definition for 'polygon'
legend.gradient: no visible global function definition for 'text'
quick.map: no visible global function definition for 'heat.colors'
quick.map: no visible global function definition for 'image'
raster.from.asc: no visible global function definition for 'raster'
raster.from.asc: no visible global function definition for
'projection<-'
raster.from.asc: no visible global function definition for 'setValues'
slope: no visible global function definition for 'setValues'
sp.from.asc: no visible global function definition for 'CRS'
sp.from.asc: no visible global function definition for 'GridTopology'
sp.from.asc: no visible global function definition for
'SpatialGridDataFrame'
Undefined global functions or variables:
CRS GridTopology SpatialGridDataFrame aggregate contour getValues
gray heat.colors image na.omit pnorm polygon projection<- quantile
rainbow raster rect sd segments setValues terrain.colors text
Consider adding
importFrom("grDevices", "gray", "heat.colors", "rainbow",
"terrain.colors")
importFrom("graphics", "contour", "image", "polygon", "rect",
"segments", "text")
importFrom("stats", "aggregate", "na.omit", "pnorm", "quantile", "sd")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File 'SDMTools/libs/SDMTools.so':
Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'

It is good practice to register native routines and to disable symbol
search.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
'/00check.log'
for details.



Installation log: 00install.out

Distribution log

SVN checkout/GIT clone log


Build log for Mac OS X 10.5 (R 2.16.x)

* installing *source* package 'SDMTools' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ConnectedComponentLabelling.c -o ConnectedComponentLabelling.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c getmin.c -o getmin.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c movewindow.c -o movewindow.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c patchstats.c -o patchstats.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c pointinpolygon.c -o pointinpolygon.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c slope.aspect.c -o slope.aspect.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c vincenty.geodesics.c -o vincenty.geodesics.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o SDMTools.so ConnectedComponentLabelling.o getmin.o movewindow.o patchstats.o pointinpolygon.o slope.aspect.o vincenty.geodesics.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Tiger/Builds/rforge/Rlib/osx9-2.16/SDMTools/libs/i386
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ConnectedComponentLabelling.c -o ConnectedComponentLabelling.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c getmin.c -o getmin.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c movewindow.c -o movewindow.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c patchstats.c -o patchstats.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c pointinpolygon.c -o pointinpolygon.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c slope.aspect.c -o slope.aspect.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c vincenty.geodesics.c -o vincenty.geodesics.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o SDMTools.so ConnectedComponentLabelling.o getmin.o movewindow.o patchstats.o pointinpolygon.o slope.aspect.o vincenty.geodesics.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Tiger/Builds/rforge/Rlib/osx9-2.16/SDMTools/libs/ppc
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c ConnectedComponentLabelling.c -o ConnectedComponentLabelling.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c getmin.c -o getmin.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c movewindow.c -o movewindow.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c patchstats.c -o patchstats.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c pointinpolygon.c -o pointinpolygon.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c slope.aspect.c -o slope.aspect.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/usr/local/include -fPIC -g -O2 -c vincenty.geodesics.c -o vincenty.geodesics.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o SDMTools.so ConnectedComponentLabelling.o getmin.o movewindow.o patchstats.o pointinpolygon.o slope.aspect.o vincenty.geodesics.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Tiger/Builds/rforge/Rlib/osx9-2.16/SDMTools/libs/x86_64
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - ppc
*** arch - x86_64
packaged installation of 'SDMTools' as 'SDMTools_1.1-10.tgz'

* DONE (SDMTools)

Build log for Windows 7 (R 3.0.x)

(SDMTools 1.1-13)
* installing to library 'z:/rforge/Rlib/win7-3.0'
* installing *source* package 'SDMTools' ...
** libs

*** arch - i386
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c ConnectedComponentLabelling.c -o ConnectedComponentLabelling.o
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c getmin.c -o getmin.o
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c movewindow.c -o movewindow.o
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c patchstats.c -o patchstats.o
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c pointinpolygon.c -o pointinpolygon.o
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c slope.aspect.c -o slope.aspect.o
gcc -m32 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c vincenty.geodesics.c -o vincenty.geodesics.o
gcc -m32 -shared -s -static-libgcc -o SDMTools.dll tmp.def ConnectedComponentLabelling.o getmin.o movewindow.o patchstats.o pointinpolygon.o slope.aspect.o vincenty.geodesics.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/r/r-3.0/bin/i386 -lR
installing to z:/rforge/Rlib/win7-3.0/SDMTools/libs/i386

*** arch - x64
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c ConnectedComponentLabelling.c -o ConnectedComponentLabelling.o
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c getmin.c -o getmin.o
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c movewindow.c -o movewindow.o
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c patchstats.c -o patchstats.o
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c pointinpolygon.c -o pointinpolygon.o
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c slope.aspect.c -o slope.aspect.o
gcc -m64 -I"C:/PROGRA~1/r/r-3.0/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c vincenty.geodesics.c -o vincenty.geodesics.o
gcc -m64 -shared -s -static-libgcc -o SDMTools.dll tmp.def ConnectedComponentLabelling.o getmin.o movewindow.o patchstats.o pointinpolygon.o slope.aspect.o vincenty.geodesics.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/r/r-3.0/bin/x64 -lR
installing to z:/rforge/Rlib/win7-3.0/SDMTools/libs/x64
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* MD5 sums
packaged installation of 'SDMTools' as SDMTools_1.1-13.zip
* DONE (SDMTools)