• using R Under development (unstable) (2024-12-20 r87452)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-8) 14.2.0     GNU Fortran (Debian 14.2.0-8) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• 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 ... INFO Package suggested but not available for checking: ‘mlt.docreg’
• 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 ... 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 ... [1s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
• checking loading without being on the library search path ... [1s/2s] 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 ... [14s/19s] OK
• checking Rd files ... [1s/1s] 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 ... [27s/32s] OK Examples with CPU (user + system) or elapsed time > 5s               user system elapsed tram-methods 6.220 0.039 6.906 mmlt 4.316 0.059 5.115 Coxph 4.235 0.070 5.292
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [183s/214s] OK   Running ‘Coxph-Ex.R’ [9s/11s]   Comparing ‘Coxph-Ex.Rout’ to ‘Coxph-Ex.Rout.save’ ... OK   Running ‘KaplanMeier-Ex.R’ [2s/2s]   Running ‘PI_OVL-Ex.R’ [2s/3s]   Running ‘Polr-Ex.R’ [2s/2s]   Comparing ‘Polr-Ex.Rout’ to ‘Polr-Ex.Rout.save’ ... OK   Running ‘Survreg-Ex.R’ [3s/3s]   Comparing ‘Survreg-Ex.Rout’ to ‘Survreg-Ex.Rout.save’ ... OK   Running ‘bugfixes.R’ [36s/43s]   Running ‘intercepts-Ex.R’ [3s/3s]   Comparing ‘intercepts-Ex.Rout’ to ‘intercepts-Ex.Rout.save’ ... OK   Running ‘mmlt-Ex.R’ [80s/93s]   Comparing ‘mmlt-Ex.Rout’ to ‘mmlt-Ex.Rout.save’ ... OK   Running ‘mmlt-interface.R’ [27s/32s]   Running ‘mtram-Ex.R’ [10s/11s]   Comparing ‘mtram-Ex.Rout’ to ‘mtram-Ex.Rout.save’ ... OK   Running ‘stram-Ex.R’ [9s/10s]   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 ... [306s/362s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘mtram.Rnw’ using knitr ** Processing: figure/mtram-toenail_OR_2-1.png 1800x1200 pixels, 3x8 bits/pixel, RGB Input IDAT size = 260592 bytes Input file size = 261042 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0   zc = 9 zm = 8 zs = 1 f = 0   zc = 1 zm = 8 zs = 2 f = 0   zc = 9 zm = 8 zs = 3 f = 0   zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 234718   zc = 9 zm = 8 zs = 1 f = 5   zc = 1 zm = 8 zs = 2 f = 5   zc = 9 zm = 8 zs = 3 f = 5                                 Selecting parameters:   zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 234718 Output IDAT size = 234718 bytes (25874 bytes decrease) Output file size = 234796 bytes (26246 bytes = 10.05% decrease) Quitting from lines 1965-2000 [mtram-funs] (mtram.Rnw) Error: processing vignette 'mtram.Rnw' failed with diagnostics: $ operator is invalid for atomic vectors --- failed re-building ‘mtram.Rnw’ --- re-building ‘tram.Rnw’ using knitr warning: solve(): system is singular; attempting approx solution warning: solve(): system is singular (rcond: 1.92626e-18); attempting approx solution --- finished re-building ‘tram.Rnw’ SUMMARY: processing the following file failed:   ‘mtram.Rnw’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR