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 |
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