* using log directory ‘/srv/hornik/tmp/CRAN_pretest/Epi.Rcheck’
* using R Under development (unstable) (2024-11-23 r87366)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.1 (1)
    Debian flang-new version 19.1.1 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘Epi/DESCRIPTION’ ... OK
* this is package ‘Epi’ version ‘2.58’
* checking CRAN incoming feasibility ... [5s/7s] NOTE
Maintainer: ‘Bendix Carstensen <b@bxc.dk>’

Found the following (possibly) invalid file URIs:
  URI: aaflup.pdf
    From: inst/doc/index.html
  URI: flup.R
    From: inst/doc/index.html
  URI: addLexis.pdf
    From: inst/doc/index.html
  URI: addLexis.R
    From: inst/doc/index.html
  URI: crisk.pdf
    From: inst/doc/index.html
  URI: crisk.R
    From: inst/doc/index.html
  URI: simLexis.pdf
    From: inst/doc/index.html
  URI: simLexis.R
    From: inst/doc/index.html
  URI: yll.pdf
    From: inst/doc/index.html
  URI: yll.R
    From: inst/doc/index.html
* 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 ‘Epi’ can be installed ... [10s/10s] OK
* used C compiler: ‘Debian clang version 19.1.3 (2)’
* checking package directory ... OK
* checking for future file timestamps ... 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/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [19s/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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘fixall.bat’ ‘mvall.bat’ ‘rwall.bat’
* checking examples ... [27s/27s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... WARNING
Failed to locate ‘weave’ output file ‘aaflup.pdf’ or ‘aaflup.html’ for vignette with name ‘aaflup’ and engine ‘utils::Sweave’. The following files exist in working directory ‘/srv/hornik/tmp/CRAN_pretest/Epi.Rcheck/00_pkg_src/Epi/inst/doc’: ‘index.html’ (1665 bytes)Failed to locate ‘weave’ output file ‘addLexis.pdf’ or ‘addLexis.html’ for vignette with name ‘addLexis’ and engine ‘utils::Sweave’. The following files exist in working directory ‘/srv/hornik/tmp/CRAN_pretest/Epi.Rcheck/00_pkg_src/Epi/inst/doc’: ‘index.html’ (1665 bytes)Failed to locate ‘weave’ output file ‘crisk.pdf’ or ‘crisk.html’ for vignette with name ‘crisk’ and engine ‘utils::Sweave’. The following files exist in working directory ‘/srv/hornik/tmp/CRAN_pretest/Epi.Rcheck/00_pkg_src/Epi/inst/doc’: ‘index.html’ (1665 bytes)Failed to locate ‘weave’ output file ‘simLexis.pdf’ or ‘simLexis.html’ for vignette with name ‘simLexis’ and engine ‘utils::Sweave’. The following files exist in working directory ‘/srv/hornik/tmp/CRAN_pretest/Epi.Rcheck/00_pkg_src/Epi/inst/doc’: ‘index.html’ (1665 bytes)Failed to locate ‘weave’ output file ‘yll.pdf’ or ‘yll.html’ for vignette with name ‘yll’ and engine ‘utils::Sweave’. The following files exist in working directory ‘/srv/hornik/tmp/CRAN_pretest/Epi.Rcheck/00_pkg_src/Epi/inst/doc’: ‘index.html’ (1665 bytes)
Package vignettes without corresponding single PDF/HTML:
  ‘aaflup.rnw’
  ‘addLexis.rnw’
  ‘crisk.rnw’
  ‘simLexis.rnw’
  ‘yll.rnw’
Package vignettes without corresponding tangle output:
  ‘aaflup.rnw’
  ‘addLexis.rnw’
  ‘crisk.rnw’
  ‘simLexis.rnw’
  ‘yll.rnw’
* checking re-building of vignette outputs ... [146s/146s] WARNING
Error(s) in re-building vignettes:
  ...
--- re-building ‘aaflup.rnw’ using Sweave

Attaching package: ‘survival’

The following object is masked from ‘package:popEpi’:

    Surv

Error: processing vignette 'aaflup.rnw' failed with diagnostics:
Running 'texi2dvi' on 'aaflup.tex' failed.
LaTeX errors:
! LaTeX Error: File `flup-dmL1' not found.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Emergency stop.
 ...                                              
                                                  
l.374 ...aphics[width = 0.35\textwidth]{flup-dmL1}
                                                  
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘aaflup.rnw’

--- re-building ‘addLexis.rnw’ using Sweave

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Joining with `by = join_by(lex.id)`
Joining with `by = join_by(lex.id)`
Joining with `by = join_by(lex.id)`
--- finished re-building ‘addLexis.rnw’

--- re-building ‘crisk.rnw’ using Sweave

Attaching package: ‘survival’

The following object is masked from ‘package:popEpi’:

    Surv

--- finished re-building ‘crisk.rnw’

--- re-building ‘simLexis.rnw’ using Sweave
--- finished re-building ‘simLexis.rnw’

--- re-building ‘yll.rnw’ using Sweave
--- finished re-building ‘yll.rnw’

SUMMARY: processing the following file failed:
  ‘aaflup.rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [6s/6s] OK
* checking HTML version of manual ... [3s/3s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 WARNINGs, 1 NOTE