R Development Page

refundDevel log file (check_x86_64_linux)

Thu Aug 18 15:55:18 2016: Checking package refundDevel (SVN revision 187) ...
* using log directory ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/refundDevel.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 ‘refundDevel/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘refundDevel’ version ‘0.3-3’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Lei Huang ’

New submission

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 Title field should be in title case, current version then in title case:
‘developer version of refund: Regression with Functional Data’
‘Developer Version of Refund: Regression with Functional Data’

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 ‘refundDevel’ 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 predict.fgam predict.pffr
  predict.pfr 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
Predict.matrix.pcre.random.effect: no visible global function
  definition for ‘model.matrix’
Predict.matrix.pcre.random.effect: no visible global function
  definition for ‘as.formula’
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’
getL : : no visible global function definition for ‘filter’
getNPC.DonohoGavish: no visible global function definition for ‘median’
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’
lf.vd: no visible global function definition for ‘getFromNamespace’
lf.vd: no visible global function definition for ‘modifyList’
lf.vd : : no visible global function definition for ‘approx’
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’
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’
Undefined global functions or variables:
  abline approx as as.formula coef col2rgb complete.cases cov dbeta
  dnorm filter fitted formula getFromNamespace 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",
             "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 ‘refundDevel-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, 3 NOTEs
See
  ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/refundDevel.Rcheck/00check.log’
for details.

Run time: 119.11 seconds.