R Development Page
gmrf log file (check_x86_64_windows)
* using log directory 'R:/run/building/build_2017-11-16-03-05/RF_PKG_CHECK/PKGS/gmrf.Rcheck'
* using R version 3.4.1 Patched (2017-09-04 r73206)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'gmrf/DESCRIPTION' ... OK
* this is package 'gmrf' version '0.0'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Patrick Brown '
New submission
The Title field is just the package name: provide a real title.
The Description field should start with a capital letter.
The Date field is over a month old.
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'gmrf' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Versioned 'LinkingTo' value for 'Matrix' is only usable in R >= 3.0.2
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
'vignettesStuff'
* 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
* loading checks for arch 'i386'
** 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 use of S3 registration ... OK
* loading checks for arch 'x64'
** 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 use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
conditionalGmrf: no visible binding for global variable 'resids'
conditionalGmrf: no visible global function definition for 'raster'
conditionalGmrf: no visible global function definition for 'values<-'
loglikGmrfOneRange: no visible global function definition for
'optimize'
Undefined global functions or variables:
optimize raster resids values<-
Consider adding
importFrom("stats", "optimize")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: summaryGmrfFitNugget.Rd:22-24: Dropping empty section \examples
* 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 ... WARNING
Functions or methods with usage in documentation object 'loglikGmrf' but not in code:
loglikGmrfNugget
Functions or methods with usage in documentation object 'summaryGmrfFitNugget' but not in code:
summaryGmrfFitNugget summaryGmrfFit
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File 'gmrf/libs/i386/gmrf.dll':
Found no calls to: 'R_registerRoutines', 'R_useDynamicSymbols'
File 'gmrf/libs/x64/gmrf.dll':
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 ...
** running examples for arch 'i386' ... ERROR
Running examples in 'gmrf-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loglikGmrf
> ### Title: Likelihood of a Gaussian Markov Random Field model
> ### Aliases: loglikGmrf loglikGmrfNugget
>
> ### ** Examples
>
>
> data('swissRainR')
>
> swissRainDf = as.data.frame(swissRainR)
> Xmat = model.matrix( ~ alt,swissRainDf)
> swissShape = 1
>
> loglikGmrf(0.8, swissRainDf[,'prec5'],
+ Xmat, swissNN, swissShape)
Error in loglikGmrf(0.8, swissRainDf[, "prec5"], Xmat, swissNN, swissShape) :
could not find function "loglikGmrf"
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'gmrf-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: loglikGmrf
> ### Title: Likelihood of a Gaussian Markov Random Field model
> ### Aliases: loglikGmrf loglikGmrfNugget
>
> ### ** Examples
>
>
> data('swissRainR')
>
> swissRainDf = as.data.frame(swissRainR)
> Xmat = model.matrix( ~ alt,swissRainDf)
> swissShape = 1
>
> loglikGmrf(0.8, swissRainDf[,'prec5'],
+ Xmat, swissNN, swissShape)
Error in loglikGmrf(0.8, swissRainDf[, "prec5"], Xmat, swissNN, swissShape) :
could not find function "loglikGmrf"
Execution halted
* checking for unstated dependencies in 'tests' ... WARNING
Warning: parse error in file 'gmrfSim.R':
191:18: unexpected ','
190: loglikGmrfGivenQ(
191: propNugget=0),
^
'::' or ':::' imports not declared from:
'MODIS' 'RColorBrewer'
'library' or 'require' calls not declared from:
'R.utils' 'mapmisc' 'mgcv'
* checking tests ...
** running tests for arch 'i386' ...
Running 'gmrfC.R'
Warning message:
running command '"R:/lib/R/R-PATC~1/bin/i386/R" CMD BATCH --vanilla "gmrfC.R" "gmrfC.Rout"' had status 1
ERROR
Running the tests in 'tests/gmrfC.R' failed.
Last 13 lines of output:
Loading required package: raster
Loading required package: sp
>
>
>
> myraster = squareRaster(raster(extent(0,8000,0,6000), ncols=80,nrows=120))
> myNN = NNmat(myraster)
> myQ = maternGmrfPrec(myNN,
+ param=c(shape=2, oneminusar=0.1,
+ conditionalVariance=1),
+ adjustEdges=FALSE)
>
> themodel = attributes(myQ)$param[['theo']]
Error in attributes(myQ)$param[["theo"]] : subscript out of bounds
Execution halted
** running tests for arch 'x64' ...
Running 'gmrfC.R'
Warning message:
running command '"R:/lib/R/R-PATC~1/bin/x64/R" CMD BATCH --vanilla "gmrfC.R" "gmrfC.Rout"' had status 1
ERROR
Running the tests in 'tests/gmrfC.R' failed.
Last 13 lines of output:
Loading required package: raster
Loading required package: sp
>
>
>
> myraster = squareRaster(raster(extent(0,8000,0,6000), ncols=80,nrows=120))
> myNN = NNmat(myraster)
> myQ = maternGmrfPrec(myNN,
+ param=c(shape=2, oneminusar=0.1,
+ conditionalVariance=1),
+ adjustEdges=FALSE)
>
> themodel = attributes(myQ)$param[['theo']]
Error in attributes(myQ)$param[["theo"]] : subscript out of bounds
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 4 ERRORs, 2 WARNINGs, 6 NOTEs
See
'R:/run/building/build_2017-11-16-03-05/RF_PKG_CHECK/PKGS/gmrf.Rcheck/00check.log'
for details.
Run time: 119.34 seconds.