* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/TreePar.Rcheck’
* using R Under development (unstable) (2022-04-26 r82260)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘TreePar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TreePar’ version ‘3.3’
* 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 whether package ‘TreePar’ can be installed ... [18s/44s] OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [30s/81s] 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.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* 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 ... [7s/19s] 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])
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
TreePar
 --- call from context --- 
lambda(m, SI)
 --- call from argument --- 
infs > 0 && infs <= N
 --- R stacktrace ---
where 1: lambda(m, SI)
where 2: makeMatrix()
where 3: expm(makeMatrix() * dt)
where 4: LikDD(c(lambdavec[1], muvec[1], N), x = sort(x), model = -1, 
    root = 0, sampling = sampling)
where 5: print(LikDD(c(lambdavec[1], muvec[1], N), x = sort(x), model = -1, 
    root = 0, sampling = sampling)[1])

 --- value of length: 8 type: logical ---
[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
 --- function from context --- 
function (infs, SI) 
{
    if (infs > 0 && infs <= N) {
        if (SI == TRUE) {
            return(beta * (1 - 1 * infs/N))
        }
        else {
            return(beta)
        }
    }
    else return(0)
}
<bytecode: 0x75f0f20>
<environment: 0x75ee030>
 --- function search by body ---
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/TreePar.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 6:06.92, 128.41 + 12.28