• using R Under development (unstable) (2025-02-19 r87756)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 20.1.0-rc2     flang version 20.1.0-rc2
• 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 ‘1.2-0’
• 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 ... [19s/47s] OK See the install log for details.
• checking installed package size ... OK
• 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 ... [3s/10s] 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 ... [37s/100s] 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 ... [62s/161s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [9m/16m] NOTE   Running ‘Coxph-Ex.R’ [20s/51s]   Comparing ‘Coxph-Ex.Rout’ to ‘Coxph-Ex.Rout.save’ ... OK   Running ‘KaplanMeier-Ex.R’ [4s/11s]   Running ‘PI_OVL-Ex.R’ [5s/13s]   Running ‘Polr-Ex.R’ [4s/10s]   Comparing ‘Polr-Ex.Rout’ to ‘Polr-Ex.Rout.save’ ... OK   Running ‘Survreg-Ex.R’ [7s/16s]   Comparing ‘Survreg-Ex.Rout’ to ‘Survreg-Ex.Rout.save’ ... OK   Running ‘bugfixes.R’ [114s/255s]   Running ‘intercepts-Ex.R’ [7s/14s]   Comparing ‘intercepts-Ex.Rout’ to ‘intercepts-Ex.Rout.save’ ... OK   Running ‘mmlt-Ex.R’ [254s/418s]   Comparing ‘mmlt-Ex.Rout’ to ‘mmlt-Ex.Rout.save’ ... OK   Running ‘mmlt-interface.R’ [82s/122s]   Running ‘mtram-Ex.R’ [21s/27s]   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’ [23s/34s]   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 ... [14m/18m] OK
• checking PDF version of manual ... [8s/12s] 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