CRAN Package Check Results for Package TreePar

Last updated on 2022-04-27 11:54:13 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.3 11.51 108.88 120.39 NOTE
r-devel-linux-x86_64-debian-gcc 3.3 10.97 83.11 94.08 NOTE
r-devel-linux-x86_64-fedora-clang 3.3 142.66 ERROR
r-devel-linux-x86_64-fedora-gcc 3.3 138.38 ERROR
r-devel-windows-x86_64 3.3 28.00 123.00 151.00 NOTE
r-patched-linux-x86_64 3.3 10.67 107.60 118.27 NOTE
r-release-linux-x86_64 3.3 12.84 105.43 118.27 NOTE
r-release-macos-arm64 3.3 37.00 NOTE
r-release-macos-x86_64 3.3 68.00 NOTE
r-release-windows-x86_64 3.3 24.00 127.00 151.00 NOTE
r-oldrel-macos-arm64 3.3 53.00 NOTE
r-oldrel-macos-x86_64 3.3 70.00 NOTE
r-oldrel-windows-ix86+x86_64 3.3 26.00 119.00 145.00 NOTE

Check Details

Version: 3.3
Check: R code for possible problems
Result: NOTE
    LikAge: no visible global function definition for 'read.table'
    bd.ME.optim: no visible global function definition for 'optim'
    bd.ME.optim.rho: no visible global function definition for 'optim'
    bd.ME.optim.rho.all: no visible global function definition for 'optim'
    bd.MEyule.optim: no visible global function definition for 'optimize'
    bd.MEyule.optim: no visible global function definition for 'optim'
    bd.age.optim.matlab: no visible global function definition for
     'read.table'
    bd.groups.conf: no visible global function definition for 'uniroot'
    bd.shifts.plot: no visible global function definition for 'lines'
    bdsky.stt.optim: no visible global function definition for 'optim'
    create.mat: no visible global function definition for 'write.table'
    Undefined global functions or variables:
     lines optim optimize read.table uniroot write.table
    Consider adding
     importFrom("graphics", "lines")
     importFrom("stats", "optim", "optimize", "uniroot")
     importFrom("utils", "read.table", "write.table")
    to your NAMESPACE file.
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-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 3.3
Check: examples
Result: ERROR
    Running examples in ‘TreePar-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: LikShifts
    > ### Title: LikShifts: Calculates the likelihood of time-dependent birth and
    > ### death rates given a phylogenetic tree.
    > ### Aliases: LikShifts
    >
    > ### ** Examples
    >
    >
    > timevec<-c(0,0.15,0.25)
    > lambdavec<-c(2.5,2,3)
    > muvec<-c(0.5,0.7,0.6)
    > x<-c(0.3,0.19,0.1)
    > x1<-c(x,max(x)*1.1)
    > x2<-c(x,max(x))
    > sampling<-0.4
    > grouptime<- rep(min(x)*0.95,length(x)+1)
    > group<- cbind(grouptime,grouptime*0+1)
    > group2 <- group
    > group2[1,2] <- 4
    > group2[2,2] <- 5
    > group2[3,2] <- 3
    > group3<-group
    > group3[2,2]<-10
    >
    > ### calculate likelihoods with root = 1
    >
    > ## Shifts in speciation / extinction rates (Stadler, PNAS 2011; Smrckova & Stadler, Manuscript 2014)
    > for (survival in c(0,1)) {
    + print(LikShiftsPP(x,timevec,lambdavec,muvec,sampling,survival=survival))
    + print(LikShifts(x,timevec,lambdavec,muvec,c(sampling,1,1),survival= survival))
    + print(LikShifts(x,timevec,lambdavec,muvec,c(sampling,1,1),survival= survival,groups=group))
    + print(LikShiftsSTT(par=c(lambdavec,muvec,timevec[-1]),x,x*0+1,sprob=c(0,0,0),
    + sampling=c(sampling,0,0),survival=survival,root=1))
    + print(" ")
    + }
    [1] 2.322383
    [1] 2.322383
    grouptime
     2.322383
    [1] 2.322383
    [1] " "
    [1] 0.9337149
    [1] 0.9337149
    grouptime
    0.9337149
    [1] 0.9337149
    [1] " "
    >
    > ## Shifts in speciation / extinction rates with group sampling
    > for (survival in c(0,1)) {
    + print(LikShifts(x,timevec,lambdavec,muvec,c(sampling,1,1),survival= survival,groups=group2))
    + print(LikShifts(x,timevec,lambdavec,muvec,c(sampling,1,1),survival= survival,groups=group3))
    + print(" ")
    + }
    grouptime
     16.48329
    grouptime
     16.48329
    [1] " "
    grouptime
     15.09463
    grouptime
     15.09463
    [1] " "
    >
    > ## Constant speciation and extinction rates
    > # condition on age of tree x[1] and number of tips n
    > LikShiftsPP(x,timevec[1],lambdavec[1],muvec[1],sampling,n=1)
    [1] -1.322236
    > LikConstantn(lambdavec[1],muvec[1],sampling,x)
    [1] -1.322236
    > print(" ")
    [1] " "
    > # condition on age of tree x[1]
    > for (survival in c(0,1)) {
    + print(LikConstant(lambdavec[1],muvec[1],sampling,x,root=1,survival=survival))
    + print(LikShiftsSTT(par=c(lambdavec[1],lambdavec[1],muvec[1],muvec[1],1),x,x*0+1,
    + sprob=c(0,0),sampling=c(sampling,1),survival=survival,root=1))
    + print(LikShiftsPP(x,c(0),lambdavec[1],muvec[1],sampling,root=1,survival=survival))
    + print(LikShifts(x,c(0),lambdavec[1],muvec[1],c(sampling),survival=survival))
    + print(LikShifts(x,c(0),lambdavec[1],muvec[1],c(sampling),survival= survival,groups=group))
    + print(LikShifts(x,c(0),c(lambdavec[1],lambdavec[1],lambdavec[1]),
    + c(muvec[1],muvec[1],muvec[1]),c(sampling,1,1),survival= survival))
    + print(" ")
    + }
    [1] 2.055813
    [1] 2.055813
    [1] 2.055813
    [1] 2.055813
    grouptime
     2.055813
    [1] 2.055813
    [1] " "
    [1] 0.7345498
    [1] 0.7345498
    [1] 0.7345498
    [1] 0.7345498
    grouptime
    0.7345498
    [1] 0.7345498
    [1] " "
    >
    > ## Diversity-dependent speciation rates
    > # condition on age of tree x[1], survival = 0
    > N<-10
    > pars <- matrix(c(N,lambdavec[1],muvec[1],0,sampling),nrow=1)
    >
    > ### calculate likelihoods with root = 0
    >
    > ## Constant speciation and extinction rates
    > # condition on age of tree x[1] and number of tips n
    > print(LikShiftsPP(x,timevec[1],lambdavec[1],muvec[1],sampling,root=0,n=1))
    [1] -2.420848
    > print(LikConstantn(lambdavec[1],muvec[1],sampling,x,root=0))
    [1] -2.420848
    > print(" ")
    [1] " "
    > # condition on age of tree x[1]
    > for (survival in c(0,1)){
    + print(LikShiftsPP(x,c(0),lambdavec[1],muvec[1],sampling,root=0,survival=survival))
    + print(LikConstant(lambdavec[1],muvec[1],sampling,x,root=0,survival=survival))
    + print(" ")
    + }
    [1] 1.050841
    [1] 1.050841
    [1] " "
    [1] 0.390209
    [1] 0.390209
    [1] " "
    > ## Diversity-dependent speciation rates
    > # condition on age of tree x[1], survival = 0
    > print(LikDD(c(lambdavec[1],muvec[1],N),x=sort(x),model=-1,root=0,sampling=sampling)[1])
    Error in h(simpleError(msg, call)) :
     error in evaluating the argument 'x' in selecting a method for function 'print': error in evaluating the argument 'x' in selecting a method for function 'expm': 'length = 8' in coercion to 'logical(1)'
    Calls: print ... lambda -> .handleSimpleError -> h -> .handleSimpleError -> h
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc