* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/treestats.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* 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 ‘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 ... [147s/448s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/treestats-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 ... [15s/57s] 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 ... [29s/160s] OK
Running ‘testthat.R’ [28s/156s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [2m/17m] ERROR
Error(s) in re-building vignettes:
--- re-building ‘Example_abc.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/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 = 13078 bytes
Input file size = 13948 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11302
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11263
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 = 11263
Output IDAT size = 11263 bytes (1815 bytes decrease)
Output file size = 11341 bytes (2607 bytes = 18.69% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/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 = 21129 bytes
Input file size = 22011 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19680
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 19482
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 = 19482
Output IDAT size = 19482 bytes (1647 bytes decrease)
Output file size = 19560 bytes (2451 bytes = 11.14% 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-devel/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-devel/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 ... [9s/13s] OK
* checking HTML version of manual ... [4s/16s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR