* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/tram.Rcheck’
* using R Under development (unstable) (2025-02-25 r87819)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘tram/DESCRIPTION’ ... OK
* this is package ‘tram’ version ‘1.2-1’
* package encoding: UTF-8
* 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 ‘tram’ can be installed ... [17s/21s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/tram-00install.html' for details.
* checking package directory ... 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 ... 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 ... [31s/36s] OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [60s/65s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [415s/418s] NOTE
  Running ‘Coxph-Ex.R’ [21s/22s]
  Comparing ‘Coxph-Ex.Rout’ to ‘Coxph-Ex.Rout.save’ ... OK
  Running ‘KaplanMeier-Ex.R’
  Running ‘PI_OVL-Ex.R’
  Running ‘Polr-Ex.R’
  Comparing ‘Polr-Ex.Rout’ to ‘Polr-Ex.Rout.save’ ... OK
  Running ‘Survreg-Ex.R’
  Comparing ‘Survreg-Ex.Rout’ to ‘Survreg-Ex.Rout.save’ ... OK
  Running ‘bugfixes.R’ [95s/96s]
  Running ‘intercepts-Ex.R’
  Comparing ‘intercepts-Ex.Rout’ to ‘intercepts-Ex.Rout.save’ ... OK
  Running ‘mmlt-Ex.R’ [191s/193s]
  Comparing ‘mmlt-Ex.Rout’ to ‘mmlt-Ex.Rout.save’ ... OK
  Running ‘mmlt-interface.R’ [46s/47s]
  Running ‘mtram-Ex.R’ [21s/21s]
  Comparing ‘mtram-Ex.Rout’ to ‘mtram-Ex.Rout.save’ ...11,17d10
< Warning messages:
< 1: In optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower,  :
<   convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
< 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
<   unable to evaluate scaled gradient
< 3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
<   Model failed to converge: degenerate  Hessian with 1 negative eigenvalues
27c20
< 'log Lik.' -Inf (df=6)
---
> 'log Lik.' -876 (df=6)
34c27
< [1] 0.041
---
> [1] 0.039
43c36
<      -10.38        0.43 
---
>       -9.82        0.41 
51c44
< [1] 1 0 1
---
> [1] 0.929 0.018 0.223
60,61c53,54
< [1,]  506   10
< [2,]   10   29
---
> [1,]  565   11
> [2,]   11   33
68,69c61,62
< (Intercept)         587    0
< Days                  0  587
---
> (Intercept)         565   11
> Days                 11   33
72c65
<          24          24 
---
>        23.8         5.7 
75,76c68,69
< (Intercept)           1    0
< Days                  0    1
---
> (Intercept)       1.000 0.081
> Days              0.081 1.000
  Running ‘stram-Ex.R’ [16s/16s]
  Comparing ‘stram-Ex.Rout’ to ‘stram-Ex.Rout.save’ ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [409s/413s] OK
* checking PDF version of manual ... OK
* checking HTML 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 NOTE