* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/tram.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 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 ... 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 ... OK
See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/tram-00install.html' 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/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 ... [20s/25s] 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 ... [38s/44s] OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
tram-methods 7.940  0.079   8.812
mmlt         7.022  0.072   8.641
perm_test    5.560  0.130   6.744
Coxph        5.229  0.071   6.383
mtram        5.216  0.051   5.986
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [302s/379s] OK
  Running ‘Coxph-Ex.R’ [13s/16s]
  Comparing ‘Coxph-Ex.Rout’ to ‘Coxph-Ex.Rout.save’ ... OK
  Running ‘KaplanMeier-Ex.R’ [2s/3s]
  Running ‘PI_OVL-Ex.R’ [3s/4s]
  Running ‘Polr-Ex.R’ [2s/3s]
  Comparing ‘Polr-Ex.Rout’ to ‘Polr-Ex.Rout.save’ ... OK
  Running ‘Survreg-Ex.R’ [4s/6s]
  Comparing ‘Survreg-Ex.Rout’ to ‘Survreg-Ex.Rout.save’ ... OK
  Running ‘bugfixes.R’ [62s/78s]
  Running ‘intercepts-Ex.R’ [4s/5s]
  Comparing ‘intercepts-Ex.Rout’ to ‘intercepts-Ex.Rout.save’ ... OK
  Running ‘mmlt-Ex.R’ [140s/181s]
  Comparing ‘mmlt-Ex.Rout’ to ‘mmlt-Ex.Rout.save’ ... OK
  Running ‘mmlt-interface.R’ [44s/53s]
  Running ‘mtram-Ex.R’ [15s/17s]
  Comparing ‘mtram-Ex.Rout’ to ‘mtram-Ex.Rout.save’ ... OK
  Running ‘stram-Ex.R’ [12s/14s]
  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 ... [153s/180s] 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 1329-1334 [mtram-toenail_glmer_RS] (mtram.Rnw)
Error: processing vignette 'mtram.Rnw' failed with diagnostics:
PIRLS loop resulted in NaN value
--- failed re-building ‘mtram.Rnw’

--- re-building ‘tram.Rnw’ using knitr
--- 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 ... [5s/7s] OK
* checking HTML version of manual ... [2s/3s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR