R Development Page
refund log file (check_x86_64_linux)
Thu Aug 18 15:32:37 2016: Checking package refund (SVN revision 178) ...
* using log directory ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/refund.Rcheck’
* using R version 3.3.1 Patched (2016-08-17 r71112)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘refund/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘refund’ version ‘0.1-11’
* checking CRAN incoming feasibility ... WARNING
Maintainer: ‘Lei Huang ’
Insufficient package version (submitted: 0.1.11, existing: 0.1.16)
Found the following (possibly) invalid URLs:
URL: http://courses2.cit.cornell.edu/mwmclean (moved to https://courses2.cit.cornell.edu/mwmclean)
From: man/af.Rd
man/fgam.Rd
man/vis.fgam.Rd
Status: 404
Message: Not Found
URL: http://www.columbia.edu/~yw2016/Marginal Spline6.pdf
From: man/coef.pffr.Rd
Status: 404
Message: Not Found
URL contains spaces
Spaces in an http[s] URL should probably be replaced by %20
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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘refund’ can be installed ... [6s/6s] 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 use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
coef.pffr fitted.pffr model.matrix.pffr plot.fosr plot.fosr.perm
plot.fpcr plot.lpeer plot.peer plot.pffr plot.wcr plot.wnet
predict.fgam predict.pffr predict.pfr predict.wnet print.summary.pffr
residuals.pffr summary.pffr
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
af: no visible binding for global variable ‘filter’
af: no visible global function definition for ‘getFromNamespace’
af: no visible global function definition for ‘modifyList’
ccb.fpc: no visible global function definition for ‘var’
ccb.fpc: no visible global function definition for ‘quantile’
coef.pffr : getCoefs : makeDataGrid : : no visible global
function definition for ‘approx’
coef.pffr : getCoefs: no visible global function definition for
‘formula’
coef.pffr: no visible global function definition for ‘predict’
coef.pffr: no visible global function definition for ‘residuals’
coefboot.pffr : bootfct.resample: no visible global function definition
for ‘coef’
coefboot.pffr : bootfct.resid: no visible global function definition
for ‘coef’
coefboot.pffr : bootfct.residc: no visible global function definition
for ‘coef’
coefboot.pffr: no visible global function definition for ‘coef’
fbps: no visible global function definition for ‘optim’
ff: no visible binding for global variable ‘filter’
ff: no visible global function definition for ‘getFromNamespace’
ff: no visible global function definition for ‘modifyList’
ffpcplot: no visible global function definition for ‘layout’
ffpcplot: no visible global function definition for ‘abline’
ffpcplot: no visible global function definition for ‘polygon’
ffpcplot: no visible binding for global variable ‘rgb’
ffpcplot: no visible global function definition for ‘col2rgb’
ffpcplot: no visible global function definition for ‘persp’
fgam: no visible global function definition for ‘terms.formula’
fosr: no visible global function definition for ‘var’
fosr: no visible global function definition for ‘cov’
fosr.perm.fit: no visible binding for global variable ‘var’
fosr.perm.fit: no visible binding for global variable ‘median’
fosr.perm.test: no visible global function definition for ‘quantile’
fosr2s: no visible global function definition for ‘cov’
fosr2s: no visible global function definition for ‘fitted’
fpca.face: no visible global function definition for ‘smooth.spline’
fpca.face: no visible global function definition for ‘predict’
fpca.face: no visible global function definition for ‘optim’
fpca.sc: no visible global function definition for ‘predict’
fpca.sc: no visible global function definition for ‘quantile’
fpca.ssvd: no visible global function definition for ‘par’
fpca.ssvd: no visible global function definition for ‘predict’
fpca.ssvd: no visible global function definition for ‘smooth.spline’
fpca.ssvd: no visible global function definition for ‘optimize’
fpca.ssvd: no visible global function definition for ‘layout’
fpca2s: no visible global function definition for ‘smooth.spline’
fpcr.setup: no visible global function definition for ‘lm’
getNPC.DonohoGavish: no visible global function definition for ‘median’
getRsq: no visible global function definition for ‘var’
irreg2mat: no visible global function definition for ‘complete.cases’
irreg2mat: no visible global function definition for ‘filter’
lf: no visible binding for global variable ‘filter’
lf: no visible global function definition for ‘getFromNamespace’
lf: no visible global function definition for ‘modifyList’
lofocv: no visible global function definition for ‘optimize’
lpeer: no visible binding for global variable ‘sd’
lpeer: no visible global function definition for ‘as.formula’
lpfr: no visible global function definition for ‘predict’
lpfr: no visible global function definition for ‘quantile’
lw.test: no visible global function definition for ‘cov’
lw.test: no visible global function definition for ‘pnorm’
model.matrix.pffr: no visible global function definition for ‘predict’
pffr: no visible global function definition for ‘terms.formula’
pffr : : : no visible global function definition
for ‘approx’
pffrGLS: no visible global function definition for ‘terms.formula’
pffrGLS: no visible global function definition for ‘as’
pffrGLS: no visible global function definition for ‘predict’
pffrSim : rf: no visible global function definition for ‘rnorm’
pffrSim: no visible global function definition for ‘dbeta’
pffrSim: no visible global function definition for ‘rnorm’
pffrSim: no visible global function definition for ‘dnorm’
pffrSim: no visible global function definition for ‘sd’
plot.fosr: no visible global function definition for ‘par’
plot.fosr: no visible global function definition for ‘plot’
plot.fosr: no visible global function definition for ‘lines’
plot.fosr: no visible global function definition for ‘abline’
plot.fosr.perm: no visible global function definition for ‘abline’
plot.fosr.perm: no visible global function definition for ‘lines’
plot.fpcr: no visible global function definition for ‘plot’
plot.lpeer: no visible global function definition for ‘par’
plot.lpeer: no visible global function definition for ‘qnorm’
plot.lpeer: no visible global function definition for ‘abline’
plot.peer: no visible global function definition for ‘qnorm’
plot.peer: no visible global function definition for ‘abline’
plot.wcr: no visible global function definition for ‘plot’
plot.wcr: no visible global function definition for ‘par’
plot.wnet: no visible global function definition for ‘plot’
plot.wnet: no visible global function definition for ‘par’
predict.fgam : : no visible global function definition for
‘formula’
predict.pffr : : no visible global function definition for
‘formula’
predict.pffr: no visible global function definition for ‘approx’
print.summary.pffr: no visible global function definition for
‘printCoefmat’
rlrt.pfr: no visible global function definition for ‘rchisq’
sff: no visible binding for global variable ‘filter’
sff: no visible global function definition for ‘getFromNamespace’
sff: no visible global function definition for ‘modifyList’
smooth.construct.pcre.smooth.spec: no visible global function
definition for ‘as.formula’
smooth.construct.pcre.smooth.spec: no visible global function
definition for ‘model.matrix’
vis.fgam: no visible global function definition for ‘heat.colors’
vis.fgam: no visible global function definition for ‘terms’
vis.fgam: no visible binding for global variable ‘na.exclude’
vis.fgam: no visible global function definition for ‘par’
vis.fgam: no visible global function definition for ‘plot’
vis.fgam: no visible global function definition for ‘lines’
vis.fgam: no visible global function definition for ‘abline’
waveletGetCV: no visible binding for global variable ‘median’
waveletGetCV: no visible binding for global variable ‘sd’
wcr: no visible binding for global variable ‘var’
wcr: no visible global function definition for ‘cov’
wcr: no visible global function definition for ‘lm’
wcr: no visible global function definition for ‘glm’
wnet: no visible binding for global variable ‘var’
wnet: no visible global function definition for ‘predict’
Undefined global functions or variables:
abline approx as as.formula coef col2rgb complete.cases cov dbeta
dnorm filter fitted formula getFromNamespace glm heat.colors layout
lines lm median model.matrix modifyList na.exclude optim optimize par
persp plot pnorm polygon predict printCoefmat qnorm quantile rchisq
residuals rgb rnorm sd smooth.spline terms terms.formula var
Consider adding
importFrom("grDevices", "col2rgb", "heat.colors", "rgb")
importFrom("graphics", "abline", "layout", "lines", "par", "persp",
"plot", "polygon")
importFrom("methods", "as")
importFrom("stats", "approx", "as.formula", "coef", "complete.cases",
"cov", "dbeta", "dnorm", "filter", "fitted", "formula",
"glm", "lm", "median", "model.matrix", "na.exclude",
"optim", "optimize", "pnorm", "predict", "printCoefmat",
"qnorm", "quantile", "rchisq", "residuals", "rnorm", "sd",
"smooth.spline", "terms", "terms.formula", "var")
importFrom("utils", "getFromNamespace", "modifyList")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in ‘refund-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fosr
> ### Title: Function-on-scalar regression
> ### Aliases: fosr
>
> ### ** Examples
>
> require(fda)
> # The first two lines, adapted from help(fRegress) in package fda,
> # set up a functional data object representing daily average
> # temperatures at 35 sites in Canada
> daybasis25 <- create.fourier.basis(rangeval=c(0, 365), nbasis=25,
+ axes=list('axesIntervals'))
> Temp.fd <- with(CanadianWeather, smooth.basisPar(day.5,
+ dailyAv[,,'Temperature.C'], daybasis25)$fd)
>
> modmat = cbind(1, model.matrix(~ factor(CanadianWeather$region) - 1))
> constraints = matrix(c(0,1,1,1,1), 1)
>
> # Penalized OLS with smoothing parameter chosen by grid search
> olsmod = fosr(fdobj = Temp.fd, X = modmat, con = constraints, method="OLS", lambda=100*10:30)
Calculating CV for candidate smoothing parameter values...
lambda LOFO-CV
[1,] 1000 6613.443
[2,] 1100 6613.419
[3,] 1200 6613.398
[4,] 1300 6613.381
[5,] 1400 6613.368
[6,] 1500 6613.356
[7,] 1600 6613.348
[8,] 1700 6613.341
[9,] 1800 6613.337
[10,] 1900 6613.334
[11,] 2000 6613.333
[12,] 2100 6613.333
[13,] 2200 6613.335
[14,] 2300 6613.338
[15,] 2400 6613.342
[16,] 2500 6613.347
[17,] 2600 6613.353
[18,] 2700 6613.360
[19,] 2800 6613.368
[20,] 2900 6613.376
[21,] 3000 6613.385
Error in if (sum(fix.ind)) { : argument is not interpretable as logical
Calls: fosr -> amc -> fitter -> do.call -> gam.setup
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/refund.Rcheck/00check.log’
for details.
Run time: 116.73 seconds.