* using log directory 'd:/RCompile/CRANincoming/R-devel/Epi.Rcheck'
* using R Under development (unstable) (2024-11-23 r87366 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'Epi/DESCRIPTION' ... OK
* this is package 'Epi' version '2.58'
* checking CRAN incoming feasibility ... [15s] 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Epi' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* checking installed package size ... OK
* 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 ... 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 ... [40s] 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... 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 ... [51s] 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 'D:\RCompile\CRANincoming\R-devel\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 'D:\RCompile\CRANincoming\R-devel\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 'D:\RCompile\CRANincoming\R-devel\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 'D:\RCompile\CRANincoming\R-devel\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 'D:\RCompile\CRANincoming\R-devel\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 ... [369s] OK
* checking PDF version of manual ... [30s] OK
* checking HTML version of manual ... [26s] OK
* DONE
Status: 2 WARNINGs, 1 NOTE