- using R Under development (unstable) (2024-07-14 r86899)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 18.1.8 (1+b1)
Debian flang-new version 18.1.8 (1+b1)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘BIOMASS/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘BIOMASS’ version ‘2.1.11’
- 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 ‘BIOMASS’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... 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 ... [10s/11s] OK
- checking whether the package can be loaded with stated dependencies ... [10s/12s] OK
- checking whether the package can be unloaded cleanly ... [10s/13s] OK
- checking whether the namespace can be loaded with stated dependencies ... [10s/12s] OK
- checking whether the namespace can be unloaded cleanly ... [10s/12s] OK
- checking loading without being on the library search path ... [10s/12s] OK
- checking whether startup messages can be suppressed ... [10s/12s] 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 ... [50s/63s] OK
- checking Rd files ... [1s/1s] 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 ... [1s/1s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [11s/11s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [23s/34s] OK
Running ‘testthat.R’ [23s/33s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [28s/48s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘BIOMASS.Rmd’ using rmarkdown
Quitting from lines 61-64 [unnamed-chunk-6] (BIOMASS.Rmd)
Error: processing vignette 'BIOMASS.Rmd' failed with diagnostics:
replacement has 0 rows, data has 5766
--- failed re-building ‘BIOMASS.Rmd’
--- re-building ‘plot.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BIOMASS.Rcheck/vign_test/BIOMASS/vignettes/plot_files/figure-html/unnamed-chunk-3-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6796 bytes
Input file size = 7654 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5838
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5831
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 = 5831
Output IDAT size = 5831 bytes (965 bytes decrease)
Output file size = 5909 bytes (1745 bytes = 22.80% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BIOMASS.Rcheck/vign_test/BIOMASS/vignettes/plot_files/figure-html/unnamed-chunk-5-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29640 bytes
Input file size = 29754 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26993
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 IDAT size = 26270
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 = 5 IDAT size = 26270
Output IDAT size = 26270 bytes (3370 bytes decrease)
Output file size = 26348 bytes (3406 bytes = 11.45% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BIOMASS.Rcheck/vign_test/BIOMASS/vignettes/plot_files/figure-html/unnamed-chunk-6-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6587 bytes
Input file size = 7442 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5800
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5745
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 = 5745
Output IDAT size = 5745 bytes (842 bytes decrease)
Output file size = 5823 bytes (1619 bytes = 21.75% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BIOMASS.Rcheck/vign_test/BIOMASS/vignettes/plot_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14899 bytes
Input file size = 14989 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0
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 IDAT size = 13532
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 = 5 IDAT size = 13532
Output IDAT size = 13532 bytes (1367 bytes decrease)
Output file size = 13610 bytes (1379 bytes = 9.20% decrease)
--- finished re-building ‘plot.Rmd’
SUMMARY: processing the following file failed:
‘BIOMASS.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [9s/12s] OK
- checking HTML version of manual ... [3s/4s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR