* using log directory ‘/data/gannet/ripley/R/packages/tests-ATLAS/quokar.Rcheck’
* using R Under development (unstable) (2022-09-13 r82845)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘quokar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘quokar’ version ‘0.1.0’
* 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 ‘quokar’ can be installed ... [24s/65s] OK
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [6s/13s] OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... [6s/17s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/16s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/16s] OK
* checking loading without being on the library search path ... [5s/13s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [32s/87s] 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... 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’ ... OK
* checking examples ... [18s/44s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [39s/101s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘quokar.Rmd’ using rmarkdown
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve


Attaching package: 'dplyr'

The following object is masked from 'package:gridExtra':

    combine

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Smoothing formula not specified. Using: y ~ x
Smoothing formula not specified. Using: y ~ x
Smoothing formula not specified. Using: y ~ x
Smoothing formula not specified. Using: y ~ x
`geom_smooth()` using formula 'y ~ x'
Smoothing formula not specified. Using: y ~ x
Smoothing formula not specified. Using: y ~ x
Smoothing formula not specified. Using: y ~ x
Smoothing formula not specified. Using: y ~ x
Smoothing formula not specified. Using: y ~ x
Smoothing formula not specified. Using: y ~ x
Smoothing formula not specified. Using: y ~ x
Smoothing formula not specified. Using: y ~ x
Quitting from lines 287-288 (quokar.Rmd) 
Error: processing vignette 'quokar.Rmd' failed with diagnostics:
invalid parameters for GIG distribution: lambda=0.5, chi=-nan, psi=2
--- failed re-building ‘quokar.Rmd’

SUMMARY: processing the following file failed:
  ‘quokar.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [9s/21s] OK
* checking HTML version of manual ... NOTE
Found the following math rendering problems:
frame_fn_obs.Rd:24: Can't use function '$' in math mode in ...=r[\tau-I(r<0)]$ for $\tau \in ...
frame_fn_path.Rd:24: Can't use function '$' in math mode in ...=r[\tau-I(r<0)]$ for $\tau \in ...
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/data/gannet/ripley/R/packages/tests-ATLAS/quokar.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 10:16.89, 219.92 + 20.46