- 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 the install log 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