- using R Under development (unstable) (2024-04-21 r86458)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (Debian 13.2.0-13) 13.2.0
GNU Fortran (Debian 13.2.0-13) 13.2.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘DRomics/DESCRIPTION’ ... OK
- this is package ‘DRomics’ version ‘2.5-2’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... NOTE
Package suggested but not available for checking: ‘sva’
- 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 ‘DRomics’ 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/15s] OK
- checking whether the package can be loaded with stated dependencies ... [10s/15s] OK
- checking whether the package can be unloaded cleanly ... [10s/15s] OK
- checking whether the namespace can be loaded with stated dependencies ... [10s/19s] OK
- checking whether the namespace can be unloaded cleanly ... [11s/18s] OK
- checking loading without being on the library search path ... [11s/18s] OK
- checking whether startup messages can be suppressed ... [10s/18s] 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 ... [57s/81s] 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 ... [0s/1s] OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [50s/76s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bmdfilter 5.856 0.098 8.218
RNAseqdata 4.720 0.576 7.548
drcfit 4.918 0.010 7.240
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [173s/286s] OK
Running ‘examplewithNAvalues.R’ [10s/17s]
Running ‘examplewithRNAseq.R’ [13s/20s]
Running ‘examplewithanchoringdata.R’ [11s/19s]
Running ‘examplewithinsitudata.R’ [10s/17s]
Running ‘examplewithmetabolomic.R’ [12s/19s]
Running ‘examplewithmicroarray.R’ [12s/19s]
Running ‘examplewithnoreplicate.R’ [10s/16s]
Running ‘testAIC.R’ [10s/18s]
Running ‘test_selectgroups.R’ [10s/17s]
Running ‘testbmdcalc.R’ [11s/17s]
Running ‘testbmdplotwithgradient.R’ [10s/17s]
Running ‘testplotfit.R’ [10s/20s]
Running ‘testresidualtests.R’ [11s/18s]
Running ‘testscaling.R’ [10s/18s]
Running ‘testsensitivityplot.R’ [10s/18s]
Running ‘testthat.R’ [10s/14s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [24s/43s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘DRomics_vignette.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DRomics.Rcheck/vign_test/DRomics/vignettes/DRomics_vignette_files/figure-html/unnamed-chunk-6-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29807 bytes
Input file size = 29921 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20387
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 = 20387
Output IDAT size = 20387 bytes (9420 bytes decrease)
Output file size = 20465 bytes (9456 bytes = 31.60% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DRomics.Rcheck/vign_test/DRomics/vignettes/DRomics_vignette_files/figure-html/unnamed-chunk-8-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31545 bytes
Input file size = 31659 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23736
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 = 23736
Output IDAT size = 23736 bytes (7809 bytes decrease)
Output file size = 23814 bytes (7845 bytes = 24.78% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DRomics.Rcheck/vign_test/DRomics/vignettes/DRomics_vignette_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23824 bytes
Input file size = 23926 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 18004
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 = 18004
Output IDAT size = 18004 bytes (5820 bytes decrease)
Output file size = 18082 bytes (5844 bytes = 24.43% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DRomics.Rcheck/vign_test/DRomics/vignettes/DRomics_vignette_files/figure-html/unnamed-chunk-12-1.png
672x288 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8993 bytes
Input file size = 9860 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7856
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7849
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 = 7849
Output IDAT size = 7849 bytes (1144 bytes decrease)
Output file size = 7927 bytes (1933 bytes = 19.60% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DRomics.Rcheck/vign_test/DRomics/vignettes/DRomics_vignette_files/figure-html/unnamed-chunk-13-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 17302 bytes
Input file size = 18184 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15959
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 = 15959
Output IDAT size = 15959 bytes (1343 bytes decrease)
Output file size = 16037 bytes (2147 bytes = 11.81% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DRomics.Rcheck/vign_test/DRomics/vignettes/DRomics_vignette_files/figure-html/unnamed-chunk-15-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 16899 bytes
Input file size = 17001 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15223
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 = 15212
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 = 15212
Output IDAT size = 15212 bytes (1687 bytes decrease)
Output file size = 15290 bytes (1711 bytes = 10.06% decrease)
Quitting from lines at lines 434-439 [unnamed-chunk-16] (DRomics_vignette.Rmd)
Error: processing vignette 'DRomics_vignette.Rmd' failed with diagnostics:
could not find function "ComBat_seq"
--- failed re-building ‘DRomics_vignette.Rmd’
SUMMARY: processing the following file failed:
‘DRomics_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [8s/18s] OK
- checking HTML version of manual ... [2s/5s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR, 1 NOTE