* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dnapath.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 ‘dnapath/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dnapath’ version ‘0.7.6’
* 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 ‘dnapath’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/dnapath-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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
* checking whether the package can be unloaded cleanly ... [1s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
* checking loading without being on the library search path ... [1s/2s] 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 ... [13s/18s] OK
* checking Rd files ... [2s/3s] 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/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 ... [47s/55s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dnapath 6.400 0.047 7.349
get_reactome_pathways 6.053 0.201 6.726
run_glasso 4.660 0.014 5.499
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [11s/17s] OK
Running ‘testthat.R’ [11s/17s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [62s/123s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘introduction_to_dnapath.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dnapath.Rcheck/vign_test/dnapath/vignettes/introduction_to_dnapath_files/figure-html/unnamed-chunk-3-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 83472 bytes
Input file size = 83670 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 76968
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 = 76968
Output IDAT size = 76968 bytes (6504 bytes decrease)
Output file size = 77046 bytes (6624 bytes = 7.92% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dnapath.Rcheck/vign_test/dnapath/vignettes/introduction_to_dnapath_files/figure-html/unnamed-chunk-7-1.png
288x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25119 bytes
Input file size = 25233 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19956
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 = 19956
Output IDAT size = 19956 bytes (5163 bytes decrease)
Output file size = 20034 bytes (5199 bytes = 20.60% decrease)
Quitting from lines 221-224 [unnamed-chunk-8] (introduction_to_dnapath.Rmd)
Error: processing vignette 'introduction_to_dnapath.Rmd' failed with diagnostics:
HTTP 405 Method Not Allowed.
--- failed re-building ‘introduction_to_dnapath.Rmd’
--- re-building ‘package_data.Rmd’ using rmarkdown
--- finished re-building ‘package_data.Rmd’
SUMMARY: processing the following file failed:
‘introduction_to_dnapath.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... [6s/8s] OK
* checking HTML version of manual ... [2s/4s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR