• using R Under development (unstable) (2024-04-24 r86483)
• 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 ... [55s/40s] OK See the install log 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/22s] 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/88s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [19s/20s] OK   Running ‘testthat.R’ [19s/19s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [121s/183s] 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/11s] 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