- using R Under development (unstable) (2025-02-20 r87766)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 20.1.0-rc2
flang version 20.1.0-rc2
- 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 ... [141s/190s] OK
See the install log for details.
- used C++ compiler: ‘clang version 20.1.0-rc2’
- 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 ... [17s/48s] 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 ... [27s/55s] OK
Running ‘testthat.R’ [27s/54s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [100s/260s] 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 = 12984 bytes
Input file size = 13854 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11264
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11236
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 = 11236
Output IDAT size = 11236 bytes (1748 bytes decrease)
Output file size = 11314 bytes (2540 bytes = 18.33% 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 = 22145 bytes
Input file size = 23027 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20680
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 20479
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 = 20479
Output IDAT size = 20479 bytes (1666 bytes decrease)
Output file size = 20557 bytes (2470 bytes = 10.73% 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 ... [9s/21s] 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