R Development Page

BioCro log file (check_x86_64_linux)

Tue Dec 15 00:11:07 2015: Checking package BioCro (SVN revision 101) ...
* using log directory ‘/mnt/building/build_2015-12-15-00-05/RF_PKG_CHECK/PKGS/BioCro.Rcheck’
* using R version 3.2.3 Patched (2015-12-13 r69768)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘BioCro/DESCRIPTION’ ... OK
* this is package ‘BioCro’ version ‘0.268-0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Fernando Miguez ’
New submission

No package encoding and non-ASCII characters in the following R files:
  R/SoilEvapo.R
    39: # /*' Convert light assuming 1 mol PAR photons = 0.235 J/s Watts*/
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* 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 ‘BioCro’ can be installed ... [6s/6s] OK
* checking installed package size ... 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘alr’ ‘ialr’ ‘indfun’ ‘objFun’ ‘objFun2’ ‘objFunM’
* checking S3 generic/method consistency ... WARNING
predict:
  function(object, ...)
predict.MCMCc4photo:
  function(x, obs, burnin, kparm, theta, beta, Catm, b0, b1, stress,
           ws)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot.MCMCc4photo: no visible binding for global variable ‘niter’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘OpMaizeGro’ ‘RssMaizeGro’ ‘c3photoParms’ ‘idbpm’ ‘laiParms’ ‘stemp’
Undocumented data sets:
  ‘allocP’ ‘ausWea’ ‘maizeBioA’ ‘maizeBioB’ ‘maizeBioC’ ‘maizeBioD’
  ‘maizeBioE’ ‘parms’ ‘simA100’ ‘simAssim’ ‘simDat’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'MCMCc4photo':
MCMCc4photo
  Code: function(data, niter = 20000, op.level = 1, ivmax = 39, ialpha
                 = 0.04, ikparm = 0.7, itheta = 0.83, ibeta = 0.93, iRd
                 = 0.8, Catm = 380, b0 = 0.08, b1 = 3, stress = 1, ws =
                 c("gs", "vmax"), scale = 1, sds = c(1, 0.005, 0.5),
                 prior = c(39, 10, 0.04, 0.02, 3, 1.5))
  Docs: function(data, niter = 20000, op.level = 1, ivmax = 39, ialpha
                 = 0.04, ikparm = 0.7, itheta = 0.83, ibeta = 0.93, iRd
                 = 0.8, Catm = 380, b0 = 0.08, b1 = 3, stress = 1, ws =
                 c("gs", "vmax"), scale = 1, sds = c(1, 0.005, 0.5),
                 prior = c(39, 10, 0.04, 0.02, 3, 1))
  Mismatches in argument default values:
    Name: 'prior' Code: c(39, 10, 0.04, 0.02, 3, 1.5) Docs: c(39, 10, 0.04, 0.02, 3, 1)

Codoc mismatches from documentation object 'plot.MCMCc4photo':
plot.MCMCc4photo
  Code: function(x, x2 = NULL, x3 = NULL, plot.kind = c("trace",
                 "density", "OandF"), type = c("l", "p"), burnin = 1,
                 cols = c("blue", "green", "purple"), prior = FALSE,
                 pcol = "black", ...)
  Docs: function(x, x2 = NULL, x3 = NULL, plot.kind = c("trace",
                 "density"), type = c("l", "p"), burnin = 1, cols =
                 c("blue", "green", "purple"), prior = FALSE, pcol =
                 "black", ...)
  Mismatches in argument default values:
    Name: 'plot.kind' Code: c("trace", "density", "OandF") Docs: c("trace", "density")

Codoc mismatches from documentation object 'weach_imn':
weach_imn
  Code: function(data, ts = 1, rad.units = c("kilocalories"),
                 temp.units = c("Fahrenheit", "Celsius"), rh.units =
                 c("percent", "fraction"), ws.units = c("mph", "mps"),
                 pp.units = c("in", "mm"), ...)
  Docs: function(data, ts = 1, temp.units = c("Fahrenheit", "Celsius"),
                 rh.units = c("percent", "fraction"), ws.units =
                 c("mph", "mps"), pp.units = c("in", "mm"), ...)
  Argument names in code not in docs:
    rad.units
  Mismatches in argument names (first 3):
    Position: 3 Code: rad.units Docs: temp.units
    Position: 4 Code: temp.units Docs: rh.units
    Position: 5 Code: rh.units Docs: ws.units
weach_imn2
  Code: function(data, rad.units = c("Watt/m2"), temp.units =
                 c("Fahrenheit", "Celsius"), rh.units = c("percent",
                 "fraction"), ws.units = c("mph", "mps"), pp.units =
                 c("in", "mm"), na.chr = -99)
  Docs: function(data, temp.units = c("Fahrenheit", "Celsius"),
                 rh.units = c("percent", "fraction"), ws.units =
                 c("mph", "mps"), pp.units = c("in", "mm"), na.chr =
                 -99)
  Argument names in code not in docs:
    rad.units
  Mismatches in argument names (first 3):
    Position: 2 Code: rad.units Docs: temp.units
    Position: 3 Code: temp.units Docs: rh.units
    Position: 4 Code: rh.units Docs: ws.units

* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... WARNING
  ‘gs+qpdf’ made some significant size reductions:
     compacted ‘BioCro-Manual.pdf’ from 1313Kb to 738Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘BioGro-ET.R’
 [1s/1s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
   ‘BioCro-Manual.Rnw’ ... [0s/0s] OK
 [0s/0s] OK
* checking re-building of vignette outputs ... [17s/18s] OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 4 NOTEs
See
  ‘/mnt/building/build_2015-12-15-00-05/RF_PKG_CHECK/PKGS/BioCro.Rcheck/00check.log’
for details.


Run time: 84.91 seconds.