* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/clustTMB.Rcheck’
* using R Under development (unstable) (2025-02-14 r87716)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘clustTMB/DESCRIPTION’ ... OK
* this is package ‘clustTMB’ 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 ‘clustTMB’ can be installed ... [7m/14m] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/clustTMB-00install.html' for details.
* used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* 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 ... 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 ... [27s/42s] 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 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 ... [7s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [8m/10m] OK
  Running ‘testthat.R’ [8m/10m]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [32m/23m] ERROR
Error(s) in re-building vignettes:
--- re-building ‘CovarianceStructure.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/clustTMB.Rcheck/vign_test/clustTMB/vignettes/CovarianceStructure_files/figure-html/fig1-1.png
480x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 76121 bytes
Input file size = 76307 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 48934
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 48934

Output IDAT size = 48934 bytes (27187 bytes decrease)
Output file size = 49012 bytes (27295 bytes = 35.77% decrease)

--- finished re-building ‘CovarianceStructure.Rmd’

--- re-building ‘SpatialExMeuseData.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/clustTMB.Rcheck/vign_test/clustTMB/vignettes/SpatialExMeuseData_files/figure-html/sample-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 43472 bytes
Input file size = 43610 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 30466
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 30466

Output IDAT size = 30466 bytes (13006 bytes decrease)
Output file size = 30544 bytes (13066 bytes = 29.96% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/clustTMB.Rcheck/vign_test/clustTMB/vignettes/SpatialExMeuseData_files/figure-html/pairs-expl-1.png
576x384 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 24151 bytes
Input file size = 25033 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 22370
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 22370

Output IDAT size = 22370 bytes (1781 bytes decrease)
Output file size = 22448 bytes (2585 bytes = 10.33% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-devel/clustTMB.Rcheck/vign_test/clustTMB/vignettes/SpatialExMeuseData_files/figure-html/fig1-1.png
384x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 68130 bytes
Input file size = 68304 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 42335
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 42335

Output IDAT size = 42335 bytes (25795 bytes decrease)
Output file size = 42413 bytes (25891 bytes = 37.91% decrease)

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... 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 ERROR