- using R Under development (unstable) (2024-04-21 r86458)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 18.1.0 (rc4-1)
Debian flang-new version 18.1.0 (rc4-1)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘hmmm/DESCRIPTION’ ... OK
- this is package ‘hmmm’ version ‘1.0-4’
- 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 serialization versions ... OK
- checking whether package ‘hmmm’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... OK
- checking ‘build’ 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 code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [0s/1s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
- checking loading without being on the library search path ... [0s/0s] 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 ... [18s/22s] OK
- checking Rd files ... [1s/1s] NOTE
checkRd: (-1) hmmm.model.Rd:45: Lost braces; missing escapes or markup?
45 | with categories k_1, k_2, the joint frequencies y = {y_ij}, where i=1,...,k_1, j=1,...,k_2,
| ^
- 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 contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/0s] OK
- checking data for ASCII and uncompressed saves ... OK
- checking sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [1s/2s] ERROR
Running examples in ‘hmmm-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anova.hidden
> ### Title: anova for the class hidden
> ### Aliases: anova.hidden
> ### Keywords: package
>
> ### ** Examples
> data(drinks)
> y<-cbind(drinks$lemon.tea,drinks$orange.juice)
>
> f<-~lat*tea+lat*juice+tea*juice # lat indicates the latent variable
> fm<-c("l-l-l")
> fmargobs<-marg.list(fm,mflag="m")
> Ptr<-matrix(c(0.941, 0.199,
+ 0.059, 0.801),2,2,byrow=TRUE)
> Ptobs<-matrix(c(0.053, 0.215, 0.206, 0.001, 0.039, 0.021, 0.020, 0.176, 0.270,
+ 0.000, 0.000, 0.000, 0.048, 0.263, 0.360, 0.065, 0.053, 0.211)
+ ,2,9,byrow=TRUE)
>
> # saturated model (fsat<-~lat*tea*juice is implicit)
> model.obsf<-hmmm.model(marg=fmargobs,
+ lev=c(2,3,3),names=c("lat","tea","juice"))
> modelsat<-hidden.emfit(y,model.obsf,y.eps=0.01,maxit=10,
+ maxiter=2500,norm.diff.conv=0.001,old.tran.p=Ptr,bb=Ptobs)
Error in while (((norm.diff > norm.diff.conv) || (norm.score > norm.score.conv)) & :
missing value where TRUE/FALSE needed
Calls: hidden.emfit -> hidden.emfit.S -> hmmm.mlfit -> mphineq.fit
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [44s/52s] OK
- checking PDF version of manual ... [7s/9s] OK
- checking HTML version of manual ... [2s/3s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR, 1 NOTE