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phenopix log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2017-03-16-16-04/RF_PKG_CHECK/PKGS/phenopix.Rcheck'
* using R version 3.3.3 Patched (2017-03-06 r72339)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'phenopix/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phenopix' version '2.3'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Gianluca Filippa '

New submission

The Date field is over a month old.

Size of tarball: 6144234 bytes
* 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 'phenopix' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
* 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 ... WARNING
'library' or 'require' call not declared from: 'gtools'
'library' or 'require' call to 'gtools' in package code.
  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 ... OK
* 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 ... WARNING
Codoc mismatches from documentation object 'editExposure':
BeckFit
  Code: function(ts, uncert = FALSE, nrep = 100, ncores = "all", sf =
                 quantile(ts, probs = c(0.05, 0.95), na.rm = TRUE))
  Docs: function(exposures, image.path, coords, which)
  Argument names in code not in docs:
    ts uncert nrep ncores sf
  Argument names in docs not in code:
    exposures image.path coords which
  Mismatches in argument names (first 3):
    Position: 1 Code: ts Docs: exposures
    Position: 2 Code: uncert Docs: image.path
    Position: 3 Code: nrep Docs: coords

Codoc mismatches from documentation object 'greenExplore':
greenExplore
  Code: function(x, ...)
  Docs: function(x)
  Argument names in code not in docs:
    ...

Codoc mismatches from documentation object 'greenProcess':
greenProcess
  Code: function(ts, fit, threshold = NULL, plot = TRUE, which =
                 "light", uncert = FALSE, nrep = 100, envelope =
                 "quantiles", quantiles = c(0.1, 0.9), hydro = FALSE,
                 sf = quantile(ts, na.rm = TRUE, prob = c(0.05, 0.95)),
                 ncores = "all", ...)
  Docs: function(ts, fit, threshold = NULL, plot = TRUE, which =
                 "light", uncert = FALSE, nrep = 100, envelope =
                 "quantiles", quantiles = c(0.1, 0.9), hydro = FALSE,
                 ncores = "all", ...)
  Argument names in code not in docs:
    sf
  Mismatches in argument names:
    Position: 11 Code: sf Docs: ncores
    Position: 12 Code: ncores Docs: ...

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'editExposure':
  'BeckFit'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... WARNING
  'gs+qpdf' made some significant size reductions:
     compacted 'OCR.pdf' from 1959Kb to 442Kb
     compacted 'base.pdf' from 1791Kb to 567Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
plotExplore      24.37   0.02   24.39
greenProcess      6.56   0.03   70.59
fitted.phenopix   6.44   0.00    6.45
plot.phenopix     6.32   0.01   73.54
print.phenopix    6.26   0.00    6.25
update.phenopix   6.25   0.00    6.25
summary.phenopix  6.19   0.01   61.47
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : 
  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for vignette with name 'OCR'. The following files exist in directory '.': 'OCR.Rnw', 'OCR.aux', 'OCR.log', 'OCR.tex', 'base.Rnw', 'spatial.Rnw'
Calls: buildVignettes -> find_vignette_product
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 5 WARNINGs, 2 NOTEs
See
  'R:/run/building/build_2017-03-16-16-04/RF_PKG_CHECK/PKGS/phenopix.Rcheck/00check.log'
for details.


Run time: 359.14 seconds.