* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/mulea.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc-14 (Debian 14.2.0-16) 14.2.0
GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘mulea/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mulea’ version ‘1.1.1’
* 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 ‘mulea’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/mulea-00install.html' for details.
* used C++ compiler: ‘g++-14 (Debian 14.2.0-16) 14.2.0’
* 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 ... [3s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [2s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/4s] 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/19s] OK
* checking Rd files ... [0s/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 line endings in C/C++/Fortran sources/headers ... 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 ... [25s/75s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_graph 3.801 0.131 10.512
plot_barplot 3.076 0.097 9.356
plot_lollipop 3.122 0.011 9.022
reshape_results 2.960 0.157 9.327
plot_heatmap 3.069 0.040 10.321
run_test 1.098 0.021 12.733
ora-class 0.547 0.042 5.497
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [5s/89s] OK
Running ‘testthat.R’ [5s/89s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [20s/64s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘mulea.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/mulea.Rcheck/vign_test/mulea/vignettes/mulea_files/figure-html/lollipop_plot_ora-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 20792 bytes
Input file size = 20894 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17143
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 = 17143
Output IDAT size = 17143 bytes (3649 bytes decrease)
Output file size = 17221 bytes (3673 bytes = 17.58% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/mulea.Rcheck/vign_test/mulea/vignettes/mulea_files/figure-html/bar_plot_ora-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17844 bytes
Input file size = 17946 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14901
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 = 14901
Output IDAT size = 14901 bytes (2943 bytes decrease)
Output file size = 14979 bytes (2967 bytes = 16.53% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/mulea.Rcheck/vign_test/mulea/vignettes/mulea_files/figure-html/network_plot_ora-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45235 bytes
Input file size = 45373 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35661
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 = 35661
Output IDAT size = 35661 bytes (9574 bytes decrease)
Output file size = 35739 bytes (9634 bytes = 21.23% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/mulea.Rcheck/vign_test/mulea/vignettes/mulea_files/figure-html/heatmap_ora-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 38919 bytes
Input file size = 39045 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26103
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 = 26103
Output IDAT size = 26103 bytes (12816 bytes decrease)
Output file size = 26181 bytes (12864 bytes = 32.95% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/mulea.Rcheck/vign_test/mulea/vignettes/mulea_files/figure-html/network_plot_gsea-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 38836 bytes
Input file size = 38962 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30677
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 = 30677
Output IDAT size = 30677 bytes (8159 bytes decrease)
Output file size = 30755 bytes (8207 bytes = 21.06% decrease)
Quitting from lines 566-568 [DE1] (mulea.Rmd)
Error: processing vignette 'mulea.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘mulea.Rmd’
SUMMARY: processing the following file failed:
‘mulea.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... [5s/7s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR