CRAN Package Check Results for Package FlexParamCurve

Last updated on 2014-11-29 03:51:53.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.4-3 1.19 30.71 31.90 NOTE
r-devel-linux-x86_64-debian-gcc 1.4-3 1.15 30.19 31.34 NOTE
r-devel-linux-x86_64-fedora-clang 1.4-3 66.42 NOTE
r-devel-linux-x86_64-fedora-gcc 1.4-3 63.94 NOTE
r-devel-osx-x86_64-clang 1.4-3 58.97 NOTE
r-devel-windows-ix86+x86_64 1.4-3 4.00 39.00 43.00 NOTE
r-patched-linux-x86_64 1.4-3 1.21 31.44 32.65 NOTE
r-patched-solaris-sparc 1.4-3 362.50 NOTE
r-patched-solaris-x86 1.4-3 74.80 NOTE
r-release-linux-ix86 1.4-3 1.51 38.74 40.24 NOTE
r-release-linux-x86_64 1.4-3 1.21 31.51 32.72 NOTE
r-release-osx-x86_64-mavericks 1.4-3 NOTE
r-release-windows-ix86+x86_64 1.4-3 5.00 47.00 52.00 NOTE
r-oldrel-windows-ix86+x86_64 1.4-3 4.00 47.00 51.00 NOTE

Check Details

Version: 1.4-3
Check: DESCRIPTION meta-information
Result: NOTE
    Package listed in more than one of Depends, Imports, Suggests, Enhances:
     ‘nlme’
    A package should be listed in only one of these fields.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.4-3
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to ‘nlme’ which was already attached by Depends.
     Please remove these calls from your code.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.4-3
Check: R code for possible problems
Result: NOTE
    Found the following assignments to the global environment:
    File ‘FlexParamCurve/R/SSposnegRichards.R’:
     assign(optvarnm, valexp, .GlobalEnv)
     assign(optvarnm, valexp, .GlobalEnv)
     assign(optvarnm, valexp, .GlobalEnv)
     assign(optvarnm, valexp, .GlobalEnv)
     assign(".tmpposnegfile", 0, envir = .GlobalEnv)
     assign(optvarnm, valexp, .GlobalEnv)
    File ‘FlexParamCurve/R/change.pnparameters.R’:
     assign(pnoptnm, tmplate, .GlobalEnv)
    File ‘FlexParamCurve/R/extraF.R’:
     assign("legitmodel", "legitmodelreset", envir = .GlobalEnv)
     assign("legitmodel", 1, envir = .GlobalEnv)
     assign("legitmodel", genmodel, envir = .GlobalEnv)
     assign("legitmodel", submodel, envir = .GlobalEnv)
    File ‘FlexParamCurve/R/modpar.R’:
     assign(".paramsestimated", FALSE, envir = globalenv())
     assign(pnoptnm, valexp, .GlobalEnv)
     assign(pnoptnm, savoptions, .GlobalEnv)
     assign(pnoptnm, savoptions, .GlobalEnv)
     assign(".paramsestimated", FALSE, envir = globalenv())
     assign(pnoptnm, valexp, .GlobalEnv)
     assign(pnoptnm, valexp[1:length(valexp) - 1], .GlobalEnv)
    File ‘FlexParamCurve/R/pn.mod.compare.R’:
     assign(".modcmptemp", get(pnoptnm, envir = .GlobalEnv), .GlobalEnv)
     assign("richardsR20.lis", richardsR20.lis, .GlobalEnv)
     assign("richardsR12.lis", richardsR12.lis, .GlobalEnv)
     assign(savnm, mod, envir = .GlobalEnv)
    File ‘FlexParamCurve/R/pn.modselect.step.R’:
     assign(".modstptemp", get(pnoptnm, envir = .GlobalEnv), .GlobalEnv)
     assign("richardsR20.lis", richardsR20.lis, .GlobalEnv)
     assign("richardsR12.lis", richardsR12.lis, .GlobalEnv)
     assign("tempparam.select", submod, envir = globalenv())
     assign("tempmodnm", modname, envir = globalenv())
     assign("tempparam.select", substr(modnm, 10, 11), envir = .GlobalEnv)
     assign(modnm, eval(modname), envir = .GlobalEnv)
     assign("tempparam.select", "NONE", envir = globalenv())
     assign("pn.bestmodel.lis", currentmodel, envir = globalenv())
    File ‘FlexParamCurve/R/posnegRichardsInit.R’:
     assign(optvarnm, valexp, .GlobalEnv)
     assign(optvarnm, valexp, .GlobalEnv)
     assign(optvarnm, valexp, .GlobalEnv)
     assign(optvarnm, valexp, .GlobalEnv)
     assign(".tmpposnegfile", 0, envir = .GlobalEnv)
     assign(optvarnm, valexp, .GlobalEnv)
    
    Found the following calls to data() loading into the global environment:
    File ‘FlexParamCurve/R/SSposnegRichards.R’:
     data(posneg.data)
     data(logist.data)
    File ‘FlexParamCurve/R/change.pnparameters.R’:
     data(posneg.data)
    File ‘FlexParamCurve/R/extraF.R’:
     data(posneg.data)
    File ‘FlexParamCurve/R/extraF.nls.R’:
     data(posneg.data)
    File ‘FlexParamCurve/R/modpar.R’:
     data(posneg.data)
    File ‘FlexParamCurve/R/pn.mod.compare.R’:
     data(posneg.data)
    File ‘FlexParamCurve/R/pn.modselect.step.R’:
     data(posneg.data)
    File ‘FlexParamCurve/R/posnegRichards.eqn.R’:
     data(posneg.data)
    See section ‘Good practice’ in ‘?data’.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64

Version: 1.4-3
Check: Rd line widths
Result: NOTE
    Rd file 'FlexParamCurve-package.Rd':
     \examples lines wider than 100 characters:
     # run backwards stepwise model selection (Step 2) for logist.data object without need to run any previous functions
     # fit and plot a logistic curve (M=1) to data, note that all parameters set to equal 1 here are ignored
     modpar(logist.data$age,logist.data$mass,force4par=TRUE, pn.options = "myoptions")#create list for fixed parameters
     curve(posnegRichards.eqn(x, Asym = par[1], K = par[2], Infl = par[3], modno = 20), add= TRUE, pn.options = "myoptions")
    
    Rd file 'SSposnegRichards.Rd':
     \examples lines wider than 100 characters:
     modpar(posneg.data$age, posneg.data$mass,verbose=TRUE, pn.options = "myoptions", wide.bounds=TRUE)
     modpar(mydata$x,mydata$y,twocomponent.x=TRUE, pn.options = "myoptions") # if x of intersection unknown
     modpar(mydata$x,mydata$y,twocomponent.x=75, pn.options = "myoptions") # if x of intersection = 75
     Infl = Infl, M = M, RAsym = RAsym, Rk = Rk, Ri = Ri, RM = RM, modno = 1, pn.options = "myoptions")
    
    Rd file 'extraF.nls.Rd':
     \examples lines wider than 100 characters:
     modpar(posneg.data$age, posneg.data$mass, pn.options.name = "myoptions") #create list for fixed parameters
    
    Rd file 'logist.data.Rd':
     \examples lines wider than 100 characters:
     modpar(logist.data$age, logist.data$mass, force4par = TRUE, pn.options = "myoptions") #create list for fixed parameters
    
    Rd file 'modpar.Rd':
     \examples lines wider than 100 characters:
     modpar(mydata$x,mydata$y,twocomponent.x=TRUE, pn.options = "myoptions") # if x of intersection unknown
     modpar(mydata$x,mydata$y,twocomponent.x=75, pn.options = "myoptions") # if x of intersection = 75
     Infl = Infl, M = M, RAsym = RAsym, Rk = Rk, Ri = Ri, RM = RM, modno = 1, pn.options = "myoptions")
    
    Rd file 'penguin.data.Rd':
     \examples lines wider than 100 characters:
     fm1 <- nls(weight ~ SSposnegRichards(ckage,Asym=Asym,K=K,Infl=Infl, RAsym=RAsym,modno=31, pn.options= "myoptions"),
    
    Rd file 'posneg.data.Rd':
     \examples lines wider than 100 characters:
     modpar(posneg.data$age, posneg.data$mass, pn.options = "myoptions") #create list for fixed parameters
    
    Rd file 'posnegRichards.calls.Rd':
     \examples lines wider than 100 characters:
     modtofit <- as.character( posnegRichards.calls [[2]] [row.names(posnegRichards.calls [[2]]) == "22",] )
     modpar(posneg.data$age, posneg.data$mass, pn.options = "myoptions") #create list for fixed parameters
    
    Rd file 'posnegRichards.eqn.Rd':
     \examples lines wider than 100 characters:
     modpar(posneg.data$age, posneg.data$mass, pn.options = "myoptions") #create pnmodelparams for fixed parameters
     curve(posnegRichards.eqn(x,modno = 32, pn.options = "myoptions"), add = TRUE, col =2 , lwd = 3)
     # tweak the plot of a 3-parameter model by user specifying a lower asymptote: ie give some parameter values
     curve(posnegRichards.eqn(x,modno = 32, Asym = 3200, pn.options = "myoptions"), add = TRUE, col = 5, lwd = 3)
     # calculate y (dependent variable) for a given x for a 4-parameter Richards model, note that second curve parameters are unneeded
     # and replaced with value from pn.options. User-supplied variables over-ride those stored in pn.options object
     # plot a double-logistic curve (M=1, RM=1), note that second curve parameters are unneeded
     plot(1:200, posnegRichards.eqn(1:200, Asym = 1000, K = 0.5, Infl = 25, M = 1, RAsym = -100, Rk = 0.5, Ri = 125, RM = 1,
    
    Rd file 'tern.data.Rd':
     \examples lines wider than 100 characters:
     modpar(tern.data$ckage, tern.data$weight, force4par = TRUE, pn.options = "myoptions") #create pnmodelparams for fixed parameters
     fm1 <- nls(weight ~ SSposnegRichards(ckage,Asym=Asym,K=K,Infl=Infl,modno=32, pn.options= "myoptions"),
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64