FSATeach - Functions to support teaching fisheries stock assessment methods. - check results
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FSATeach

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Version: 0.0.1
Result: WARNING
Check time: 2018-01-24 14:28
* using log directory ''
* using R Under development (unstable) (2018-01-24 r74156)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'FSATeach/DESCRIPTION' ... OK
* this is package 'FSATeach' version '0.0.1'
* 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 serialized R objects in the sources ... OK
* checking whether package 'FSATeach' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: 'tcltk'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
catchCurveSim : ccSimPlot : makeNoYcl: no visible global function
definition for 'rnorm'
catchCurveSim : ccSimPlot : makeZYcl: no visible global function
definition for 'rnorm'
catchCurveSim : ccSimPlot : makeCatch: no visible global function
definition for 'rnorm'
catchCurveSim : ccSimPlot: no visible global function definition for
'par'
catchCurveSim : ccSimPlot: no visible global function definition for
'plot'
catchCurveSim : ccSimPlot: no visible global function definition for
'lines'
catchCurveSim : ccSimPlot: no visible global function definition for
'legend'
cohortSim : cohortSimPlot: no visible global function definition for
'par'
cohortSim : cohortSimPlot: no visible global function definition for
'plot'
growthModelSim: no visible global function definition for 'model.frame'
growthSimPlot: no visible global function definition for 'par'
growthSimPlot: no visible global function definition for 'plot'
growthSimPlot: no visible global function definition for 'lines'
leslieSim : leslieRandRun: no visible global function definition for
'runif'
leslieSim : detLeslieSimPlot : detPlot: no visible global function
definition for 'plot'
leslieSim : detLeslieSimPlot : detPlot: no visible global function
definition for 'points'
leslieSim : detLeslieSimPlot: no visible global function definition for
'par'
leslieSim : detLeslieSimPlot: no visible global function definition for
'legend'
leslieSim : randLeslieSimPlot: possible error in depletion(type =
"Leslie", res.ass$Ct, res.ass$Et, ricker.mod = ricker.mod): unused
arguments (type = "Leslie", ricker.mod = ricker.mod)
leslieSim : randLeslieSimPlot: no visible global function definition
for 'par'
leslieSim : randLeslieSimPlot: no visible global function definition
for 'plot'
leslieSim : mcLesliePlot: possible error in depletion(res.ass$Ct,
res.ass$Et, "Leslie", ricker.mod = ricker.mod): unused argument
(ricker.mod = ricker.mod)
leslieSim : mcLesliePlot: no visible global function definition for
'par'
leslieSim : mcLesliePlot: no visible global function definition for
'hist'
leslieSim : mcLesliePlot: no visible global function definition for
'abline'
leslieSim : mcLesliePlot: no visible global function definition for
'legend'
leslieSim : mcLesliePlot: no visible global function definition for
'plot'
lwModelSim : lwSimPlot: no visible global function definition for
'plot'
lwModelSim : lwSimPlot: no visible global function definition for
'lines'
lwModelSim : refresh.lw: no visible global function definition for
'par'
mrClosed1Sim : mrClosedSimPlot : popGen: no visible global function
definition for 'runif'
mrClosed1Sim : mrClosedSimPlot : graphGen: no visible global function
definition for 'par'
mrClosed1Sim : mrClosedSimPlot : graphGen: no visible global function
definition for 'hist'
mrClosed1Sim : mrClosedSimPlot : graphGen: no visible global function
definition for 'abline'
mrClosed1Sim : mrClosedSimPlot : graphGen: no visible global function
definition for 'legend'
simAgeBias: no visible global function definition for 'par'
simAgeBias: no visible global function definition for 'layout'
simAgeBias: no visible global function definition for 'frame'
simAgeBias: no visible global function definition for 'box'
simAgeBias: no visible global function definition for 'text'
simAgeBias: no visible global function definition for 'lines'
simAgeBias: no visible global function definition for 'points'
simAgeBias: no visible global function definition for 'plot'
simAgeBias: no visible global function definition for 'abline'
simAgeBias: no visible global function definition for 'locator'
simAgeBias: no visible global function definition for 'ageComp'
simLenFromAge: no visible global function definition for 'rnorm'
simLenSelectM: no visible global function definition for 'par'
simLenSelectM: no visible global function definition for 'layout'
simLenSelectM: no visible global function definition for 'frame'
simLenSelectM: no visible global function definition for 'box'
simLenSelectM: no visible global function definition for 'text'
simLenSelectM: no visible global function definition for 'plot'
simLenSelectM: no visible global function definition for 'axTicks'
simLenSelectM: no visible global function definition for 'axis'
simLenSelectM: no visible global function definition for 'mtext'
simLenSelectM: no visible global function definition for 'abline'
simLenSelectM: no visible global function definition for 'lines'
simLenSelectM: no visible global function definition for 'points'
simLenSelectM: no visible global function definition for 'locator'
simLenSelectM: no visible global function definition for 'as.formula'
simLenSelectM: no visible global function definition for 'runif'
simLenSelectP: no visible global function definition for 'dbeta'
simLenSelectP: no visible global function definition for 'plot'
simLenSelectP: no visible global function definition for 'runif'
srSim: no visible global function definition for 'model.frame'
srSimPlot: no visible global function definition for 'par'
srSimPlot: no visible global function definition for 'plot'
srSimPlot: no visible global function definition for 'points'
srSimPlot: no visible global function definition for 'abline'
srSimPlot: no visible global function definition for 'axis'
Undefined global functions or variables:
abline ageComp as.formula axTicks axis box dbeta frame hist layout
legend lines locator model.frame mtext par plot points rnorm runif
text
Consider adding
importFrom("graphics", "abline", "axTicks", "axis", "box", "frame",
"hist", "layout", "legend", "lines", "locator", "mtext",
"par", "plot", "points", "text")
importFrom("stats", "as.formula", "dbeta", "model.frame", "rnorm",
"runif")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'growthModelSim.Rd':
\usage lines wider than 90 characters:
growthModelSim(type = c("vbTypical", "vbOriginal", "vbGalucciQuinn", "vbMooij", "vbSchnute", "vbTypicalW", "vbOriginalW", "Gompertz1" ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'growthModelSim.Rd':
'vbModels'

Missing link or links in documentation object 'srSim.Rd':
'srModels'

See section 'Cross-references' in the 'Writing R Extensions' manual.

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

Status: 1 WARNING, 4 NOTEs
See
'/00check.log'
for details.



Installation log: 00install.out

Distribution log

SVN checkout/GIT clone log