- using R Under development (unstable) (2025-11-12 r89009)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
- running under: Fedora Linux 42 (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 ‘1.2-5’
- 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 ... [20s/61s] OK
See the install log 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 ... [3s/11s] OK
- checking whether the package can be unloaded cleanly ... [3s/12s] 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 ... [3s/11s] 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 ... [36s/108s] 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 line endings in shell scripts ... OK
- checking sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [66s/147s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [517s/577s] OK
Running ‘Coxph-Ex.R’ [17s/28s]
Running ‘KaplanMeier-Ex.R’
Running ‘PI_OVL-Ex.R’ [6s/12s]
Running ‘Survreg-Ex.R’
Running ‘bugfixes.R’ [118s/140s]
Running ‘intercepts-Ex.R’
Running ‘mmlt-Ex.R’ [239s/250s]
Running ‘mmlt-interface.R’ [76s/77s]
Running ‘mtram-Ex.R’ [16s/16s]
Running ‘stram-Ex.R’ [28s/28s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [23m/24m] WARNING
Error(s) in re-building vignettes:
--- re-building ‘NAMI.Rnw’ using knitr
Error: processing vignette 'NAMI.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'NAMI.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Emergency stop.
...
l.161 \DeclareMathOperator{\Chi1}{\chi^2_1}
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘NAMI.Rnw’
--- re-building ‘mtram.Rnw’ using knitr
Error: processing vignette 'mtram.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'mtram.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Emergency stop.
...
l.232 \DeclareMathOperator{\Chi1}{\chi^2_1}
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘mtram.Rnw’
--- re-building ‘survtram.Rnw’ using knitr
Warning in doTryCatch(return(expr), name, parentenv, handler) :
semi-transparency is not supported on this device: reported only once per page
Warning in doTryCatch(return(expr), name, parentenv, handler) :
semi-transparency is not supported on this device: reported only once per page
Warning in doTryCatch(return(expr), name, parentenv, handler) :
semi-transparency is not supported on this device: reported only once per page
Error: processing vignette 'survtram.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'survtram.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Emergency stop.
...
l.333 \DeclareMathOperator{\Chi1}{\chi^2_1}
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘survtram.Rnw’
--- re-building ‘tram.Rnw’ using knitr
Error: processing vignette 'tram.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tram.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! Emergency stop.
...
l.161 \DeclareMathOperator{\Chi1}{\chi^2_1}
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘tram.Rnw’
SUMMARY: processing the following files failed:
‘NAMI.Rnw’ ‘mtram.Rnw’ ‘survtram.Rnw’ ‘tram.Rnw’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [10s/10s] 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 WARNING