CRAN Package Check Results for Package paleoTS

Last updated on 2015-07-29 10:47:50.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.4-4 0.84 20.17 21.00 NOTE
r-devel-linux-x86_64-debian-gcc 0.4-4 0.90 19.72 20.62 NOTE
r-devel-linux-x86_64-fedora-clang 0.4-4 40.56 NOTE
r-devel-linux-x86_64-fedora-gcc 0.4-4 39.09 NOTE
r-devel-osx-x86_64-clang 0.4-4 34.59 OK
r-devel-windows-ix86+x86_64 0.4-4 5.00 49.00 54.00 NOTE
r-patched-linux-x86_64 0.4-4 0.85 20.47 21.32 NOTE
r-patched-solaris-sparc 0.4-4 245.10 OK
r-patched-solaris-x86 0.4-4 54.40 OK
r-release-linux-x86_64 0.4-4 0.85 20.59 21.44 NOTE
r-release-osx-x86_64-mavericks 0.4-4 OK
r-release-windows-ix86+x86_64 0.4-4 7.00 33.00 40.00 OK
r-oldrel-windows-ix86+x86_64 0.4-4 7.00 37.00 44.00 OK

Check Details

Version: 0.4-4
Check: R code for possible problems
Result: NOTE
    LRI : opt.lad: no visible global function definition for ‘lm’
    LRI : opt.lad: no visible global function definition for ‘optim’
    LRI: no visible global function definition for ‘plot’
    LRI: no visible global function definition for ‘abline’
    LRI: no visible global function definition for ‘title’
    LRI: no visible global function definition for ‘mtext’
    LRI: no visible global function definition for ‘text’
    logL.GRW: no visible global function definition for ‘dnorm’
    logL.Stasis: no visible global function definition for ‘dnorm’
    logL.URW: no visible global function definition for ‘dnorm’
    logL.covTrack: no visible global function definition for ‘dnorm’
    mle.Stasis: no visible global function definition for ‘var’
    opt.GRW: no visible global function definition for ‘optim’
    opt.RW.Mult: no visible global function definition for ‘optim’
    opt.RW.SameMs: no visible global function definition for ‘median’
    opt.RW.SameMs: no visible global function definition for ‘optim’
    opt.RW.SameVs: no visible global function definition for ‘median’
    opt.RW.SameVs: no visible global function definition for ‘optim’
    opt.Stasis: no visible global function definition for ‘optim’
    opt.URW: no visible global function definition for ‘optim’
    opt.covTrack: no visible global function definition for ‘lm’
    opt.covTrack: no visible global function definition for ‘coef’
    opt.covTrack: no visible global function definition for ‘var’
    opt.covTrack: no visible global function definition for ‘resid’
    opt.covTrack: no visible global function definition for ‘optim’
    opt.covTrack.Mult: no visible global function definition for ‘var’
    opt.covTrack.Mult: no visible global function definition for ‘optim’
    opt.joint.GRW: no visible global function definition for ‘optim’
    opt.joint.OU: no visible global function definition for ‘optim’
    opt.joint.Stasis: no visible global function definition for ‘optim’
    opt.joint.URW: no visible global function definition for ‘optim’
    opt.joint.punc: no visible binding for global variable ‘var’
    opt.joint.punc: no visible global function definition for ‘optim’
    opt.punc: no visible binding for global variable ‘var’
    opt.punc: no visible global function definition for ‘optim’
    opt.sgs: no visible global function definition for ‘var’
    opt.sgs: no visible global function definition for ‘optim’
    plot.paleoTS: no visible global function definition for ‘plot’
    plot.paleoTS: no visible global function definition for ‘polygon’
    plot.paleoTS: no visible global function definition for ‘lines’
    plot.paleoTS: no visible global function definition for ‘segments’
    plot.paleoTS: no visible global function definition for ‘points’
    plot.paleoTS: no visible global function definition for ‘mtext’
    read.paleoTS: no visible global function definition for ‘read.table’
    shifts: no visible global function definition for ‘combn’
    sim.GRW: no visible global function definition for ‘rnorm’
    sim.OU: no visible global function definition for ‘rnorm’
    sim.OU: no visible global function definition for ‘var’
    sim.Stasis: no visible global function definition for ‘rnorm’
    sim.covTrack: no visible global function definition for ‘rnorm’
    test.var.het: no visible global function definition for ‘pchisq’
    Undefined global functions or variables:
     abline coef combn dnorm lines lm median mtext optim pchisq plot
     points polygon read.table resid rnorm segments text title var
    Consider adding
     importFrom("graphics", "abline", "lines", "mtext", "plot", "points",
     "polygon", "segments", "text", "title")
     importFrom("stats", "coef", "dnorm", "lm", "median", "optim", "pchisq",
     "resid", "rnorm", "var")
     importFrom("utils", "combn", "read.table")
    to your NAMESPACE.
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-windows-ix86+x86_64

Version: 0.4-4
Check: Rd line widths
Result: NOTE
    Rd file 'as.paleoTS.Rd':
     \usage lines wider than 90 characters:
     as.paleoTS(mm, vv, nn, tt, MM = NULL, genpars = NULL, label = NULL, start.age = NULL, oldest=c("first", "last"), reset.time=TRUE)
     \examples lines wider than 100 characters:
     y <- as.paleoTS(mm=rnorm(10), vv=rep(1,10), nn=rep(25,10), tt=1:10, label="white noise time series")
    
    Rd file 'cat.paleoTS.Rd':
     \examples lines wider than 100 characters:
     # show all possible shift points for 20 samples divided into two semgments (assuming each has at least 6 samples)
    
    Rd file 'fit.sgs.Rd':
     \usage lines wider than 90 characters:
     fit.sgs(y, minb = 5, oshare = TRUE, pool = TRUE, silent = FALSE, hess = FALSE, meth = "L-BFGS-B", model = "GRW")
     opt.sgs(y, gg, cl = list(fnscale = -1), meth = "L-BFGS-B", hess = FALSE, oshare = TRUE, model = "GRW")
    
    Rd file 'fit3models.Rd':
     \examples lines wider than 100 characters:
     x2<- sim.GRW(ns=20, ms=0.2, vs=0.1) # step variance relatively low compared to sampling error == Noisy
    
    Rd file 'fitGpunc.Rd':
     \usage lines wider than 90 characters:
     fitGpunc(y, ng = 2, minb = 5, pool = TRUE, oshare = TRUE, method=c('AD', 'Joint'), silent = FALSE, hess=FALSE, ...)
     opt.punc(y, gg, cl = list(fnscale = -1), pool = TRUE, meth = "L-BFGS-B", hess = FALSE, oshare)
    
    Rd file 'opt.RW.Mult.Rd':
     \usage lines wider than 90 characters:
     opt.RW.Mult(yl, cl=list(fnscale=-1), model=c("GRW", "URW"), pool=TRUE, meth="L-BFGS-B", hess=FALSE)
    
    Rd file 'plot.paleoTS.Rd':
     \usage lines wider than 90 characters:
     plot(x, nse = 1, pool = FALSE, add = FALSE, modelFit=NULL, pch=19, lwd=1.5, ylim=NULL, ...)
    
    Rd file 'sim.OU.Rd':
     \usage lines wider than 90 characters:
     sim.OU(ns = 20, anc = 0, theta = 10, alpha = 0.3, vs = 0.1, vp = 1, nn = rep(20, ns), tt = 0:(ns-1))
    
    Rd file 'sim.covTrack.Rd':
     \usage lines wider than 90 characters:
     sim.covTrack(ns = 20, b = 1, evar = 0.1, z, nn = rep(20, times = ns), tt = 0:(ns-1), vp = 1)
    
    Rd file 'sim.punc.Rd':
     \usage lines wider than 90 characters:
     sim.punc(ns = c(10, 10), theta = c(0, 1), omega=rep(0,length(theta)), nn = rep(30, sum(ns)), tt = 0:(sum(ns)-1), vp = 1)
     sim.sgs(ns = c(20, 20, 20), theta = 0, omega = 1, ms = 1, vs = 0.1, nn=rep(30, sum(ns)), tt = 0:(sum(ns)-1), vp = 1)
     sim.GRW.shift(ns = c(10, 10), ms = c(0, 1), vs = c(0.5, 0.5), nn = rep(30, sum(ns)), tt = 0:(sum(ns)-1), vp = 1)
    
    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