- using R version 4.0.3 (2020-10-10)
- using platform: x86_64-pc-linux-gnu (64-bit)
- using session charset: UTF-8
- checking for file ‘SightabilityModel/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘SightabilityModel’ version ‘1.4.1’
- 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 serialization versions ... OK
- checking whether package ‘SightabilityModel’ can be installed ... OK
- 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 R 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 ... [16s/18s] 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 sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [18s/20s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Sight.Est 5.838 0.031 6.427
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking re-building of vignette outputs ... [187s/212s] WARNING
Error(s) in re-building vignettes:
...
--- re-building ‘MoosePopR-SightabilityPopR-Demo.Rmd’ using rmarkdown
New names:
* `Lone Cows` -> Lone.Cows
* `Cow W/1 \r\ncalf` -> Cow.W.1...calf
* `Cow W/2 calves` -> Cow.W.2.calves
* `Lone \r\ncalf` -> Lone...calf
* `Unk Age/Sex` -> Unk.Age.Sex
* ...
New names:
* `` -> ...1
New names:
* `` -> ...1
* `` -> ...2
New names:
* `` -> ...1
* `` -> ...2
New names:
* `` -> ...1
* `` -> ...2
Warning in sqrt(as.matrix(Cover[, 1:nbeta]) %*% beta.cov %*% t(as.matrix(Cover[, :
NaNs produced
Warning in cor(N.Animals, Block.Area) : the standard deviation is zero
Warning in cor(N.Animals, Block.Area) : the standard deviation is zero
Warning in cor(N.Animals, Block.Area) : the standard deviation is zero
Warning in cor(N.Animals, Block.Area) : the standard deviation is zero
--- finished re-building ‘MoosePopR-SightabilityPopR-Demo.Rmd’
--- re-building ‘RatioEstimator.pdf.asis’ using asis
--- finished re-building ‘RatioEstimator.pdf.asis’
--- re-building ‘SightabilityModel.Rnw’ using Sweave
Error: processing vignette 'SightabilityModel.Rnw' failed with diagnostics:
Running ‘texi2dvi’ on ‘SightabilityModel.tex’ failed.
LaTeX errors:
! Undefined control sequence.
<recently read> \Hy@colorlink
l.79 \begin{document}
! Undefined control sequence.
\close@pdflink ->\Hy@endcolorlink
\Hy@VerboseLinkStop \pdfendlink
l.79 \begin{document}
! Undefined control sequence.
<recently read> \Hy@colorlink
l.79 \begin{document}
! Undefined control sequence.
\close@pdflink ->\Hy@endcolorlink
\Hy@VerboseLinkStop \pdfendlink
l.79 \begin{document}
! Undefined control sequence.
<recently read> \Hy@colorlink
l.79 \begin{document}
! Undefined control sequence.
\close@pdflink ->\Hy@endcolorlink
\Hy@VerboseLinkStop \pdfendlink
l.79 \begin{document}
! Undefined control sequence.
<recently read> \Hy@colorlink
l.79 \begin{document}
! Undefined control sequence.
\close@pdflink ->\Hy@endcolorlink
\Hy@VerboseLinkStop \pdfendlink
l.79 \begin{document}
! Undefined control sequence.
<recently read> \Hy@colorlink
l.79 \begin{document}
! Undefined control sequence.
\close@pdflink ->\Hy@endcolorlink
\Hy@VerboseLinkStop \pdfendlink
l.79 \begin{document}
! Undefined control sequence.
<recently read> \Hy@colorlink
l.79 \begin{document}
! Undefined control sequence.
\close@pdflink ->\Hy@endcolorlink
\Hy@VerboseLinkStop \pdfendlink
l.79 \begin{document}
--- failed re-building 'SightabilityModel.Rnw'
SUMMARY: processing the following file failed:
‘SightabilityModel.Rnw’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 WARNING