* using log directory ‘/data/gannet/ripley/R/packages/tests-MKL/modTempEff.Rcheck’
* using R Under development (unstable) (2020-08-03 r78966)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘modTempEff/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘modTempEff’ version ‘1.5.2’
* 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 ‘modTempEff’ can be installed ... [11s/39s] OK
* checking package directory ... OK
* checking ‘build’ 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [15s/28s] NOTE
anova.modTempEff : anova.glmlist1 : <anonymous>: no visible global
  function definition for ‘formula’
anova.modTempEff : stat.anova1: no visible global function definition
  for ‘pchisq’
anova.modTempEff : stat.anova1: no visible global function definition
  for ‘pf’
plot.modTempEff: no visible global function definition for ‘lines’
plot.modTempEff: no visible global function definition for ‘dev.new’
plot.modTempEff: no visible global function definition for ‘par’
plot.modTempEff: no visible global function definition for ‘qnorm’
plot.modTempEff: no visible global function definition for ‘matplot’
plot.modTempEff: no visible global function definition for ‘polygon’
plot.modTempEff: no visible global function definition for ‘abline’
plot.modTempEff: no visible global function definition for ‘legend’
plot.modTempEff: no visible global function definition for ‘matlines’
summary.modTempEff: no visible global function definition for ‘terms’
tempeff: no visible global function definition for ‘model.response’
tempeff: no visible global function definition for ‘model.matrix’
tempeff: no visible binding for global variable ‘contrasts’
tempeff: no visible global function definition for ‘terms’
tempeff: no visible global function definition for ‘update.formula’
tempeff: no visible global function definition for ‘as.formula’
tempeff: no visible global function definition for ‘glm.fit’
tempeff: no visible global function definition for ‘poisson’
tempeff: no visible global function definition for ‘coef’
tempeff: no visible global function definition for ‘glm.control’
tempeff: no visible global function definition for ‘flush.console’
tempeff.fit: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  abline as.formula coef contrasts dev.new flush.console formula
  glm.control glm.fit legend lines matlines matplot model.matrix
  model.response par pchisq pf poisson polygon qnorm terms
  update.formula
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "legend", "lines", "matlines",
             "matplot", "par", "polygon")
  importFrom("stats", "as.formula", "coef", "contrasts", "formula",
             "glm.control", "glm.fit", "model.matrix", "model.response",
             "pchisq", "pf", "poisson", "qnorm", "terms",
             "update.formula")
  importFrom("utils", "flush.console")
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [28s/37s] WARNING
Error(s) in re-building vignettes:
--- re-building ‘modTempEff.Rnw’ using Sweave
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.
Loading required package: splines
Warning in model.matrix.default(mt, mf, contrasts) :
  non-list contrasts argument ignored
Warning: performance iteration with gam is deprecated, use bam instead
Warning in gam.fit(M, family = poisson(), fixedSteps = gam.fit.it, etastart = etastart) :
  fitted rates numerically 0 occurred
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: performance iteration with gam is deprecated, use bam instead
Warning: max number of iterations attained
Warning: performance iteration with gam is deprecated, use bam instead
Warning: Step size truncated due to divergence

Error: processing vignette 'modTempEff.Rnw' failed with diagnostics:
 chunk 6 
Error in gam.fit(M, family = poisson(), etastart = etastart) : 
  iterative weights or data non-finite in gam.fit - regularization may help. See ?gam.control.

--- failed re-building ‘modTempEff.Rnw’

SUMMARY: processing the following file failed:
  ‘modTempEff.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-MKL/modTempEff.Rcheck/00check.log’
for details.


Time 4:01.05, 109.09 + 8.06