* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/dnapath.Rcheck’
* using R Under development (unstable) (2024-04-27 r86487)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘dnapath/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dnapath’ version ‘0.7.4’
* 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 ... [59s/154s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/dnapath-00install.html' for details.
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [21s/40s] OK
* checking Rd files ... OK
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'dnapath2-package.Rd':
  ‘dnapath2-package’
* 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 ... NOTE
Auto-generated content requiring editing in Rd file 'dnapath2-package.Rd':
  \references: ‘This optional section can contain literature or other refere...’
  \seealso: ‘Optional links to other man pages’
  \examples: ‘\dontrun{      ## Optional simple examples of the most impor...’
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... 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 ... [86s/175s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [19s/40s] OK
  Running ‘testthat.R’ [19s/39s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [121s/254s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘introduction_to_dnapath.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/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: /data/gannet/ripley/R/packages/tests-devel/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  at lines 221-224 [unnamed-chunk-8] (introduction_to_dnapath.Rmd)
Error: processing vignette 'introduction_to_dnapath.Rmd' failed with diagnostics:
Can't join `x$entrezgene_id` with `y$entrezgene_id` due to incompatible
types.
ℹ `x$entrezgene_id` is a <double>.
ℹ `y$entrezgene_id` is a <character>.
--- failed re-building ‘introduction_to_dnapath.Rmd’

--- re-building ‘package_data.Rmd’ using rmarkdown

Quitting from lines  at lines 268-273 [unnamed-chunk-20] (package_data.Rmd)
Error: processing vignette 'package_data.Rmd' failed with diagnostics:
Can't join `x$entrezgene_id` with `y$entrezgene_id` due to incompatible
types.
ℹ `x$entrezgene_id` is a <double>.
ℹ `y$entrezgene_id` is a <character>.
--- failed re-building ‘package_data.Rmd’

SUMMARY: processing the following files failed:
  ‘introduction_to_dnapath.Rmd’ ‘package_data.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [10s/31s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 3 NOTEs