* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/treestats.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    clang version 20.1.0-rc3
    flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘treestats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘treestats’ version ‘1.70.5’
* 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 ‘treestats’ can be installed ... [87s/15s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/treestats-00install.html' for details.
* used C++ compiler: ‘clang version 20.1.0-rc3’
* checking installed package size ... 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 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 ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [14s/16s] OK
  Running ‘testthat.R’ [13s/16s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [53s/56s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘Example_abc.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/treestats.Rcheck/vign_test/treestats/vignettes/Example_abc_files/figure-html/plot_simpl2-1.png
576x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 12855 bytes
Input file size = 13725 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 11139
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 11111
  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 = 1  f = 0		IDAT size = 11111

Output IDAT size = 11111 bytes (1744 bytes decrease)
Output file size = 11189 bytes (2536 bytes = 18.48% decrease)

** Processing: /data/gannet/ripley/R/packages/tests-clang/treestats.Rcheck/vign_test/treestats/vignettes/Example_abc_files/figure-html/plot_simple-1.png
576x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21515 bytes
Input file size = 22397 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 19972
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 19784
  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 = 1  f = 0		IDAT size = 19784

Output IDAT size = 19784 bytes (1731 bytes decrease)
Output file size = 19862 bytes (2535 bytes = 11.32% decrease)


Quitting from lines 86-102 [sim_ddd] (Example_abc.Rmd)
Error: processing vignette 'Example_abc.Rmd' failed with diagnostics:
variable 7 appears to be constant within groups
--- failed re-building ‘Example_abc.Rmd’

--- re-building ‘Example_data.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/treestats.Rcheck/vign_test/treestats/vignettes/Example_data_files/figure-html/plot_size-1.png
576x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7446 bytes
Input file size = 8304 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 6569
  zc = 9  zm = 8  zs = 1  f = 0		IDAT size = 6549
  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 = 1  f = 0		IDAT size = 6549

Output IDAT size = 6549 bytes (897 bytes decrease)
Output file size = 6627 bytes (1677 bytes = 20.20% decrease)


Quitting from lines 61-64 [corr] (Example_data.Rmd)
Error: processing vignette 'Example_data.Rmd' failed with diagnostics:
NA/NaN/Inf in foreign function call (arg 10)
--- failed re-building ‘Example_data.Rmd’

--- re-building ‘Getting_started.Rmd’ using rmarkdown
--- finished re-building ‘Getting_started.Rmd’

--- re-building ‘Speed_improvement.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/treestats.Rcheck/vign_test/treestats/vignettes/Speed_improvement_files/figure-html/unnamed-chunk-2-1.png
576x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11064 bytes
Input file size = 11934 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 10269
  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 = 10269

Output IDAT size = 10269 bytes (795 bytes decrease)
Output file size = 10347 bytes (1587 bytes = 13.30% decrease)

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

SUMMARY: processing the following files failed:
  ‘Example_abc.Rmd’ ‘Example_data.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