* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/INCATome.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 ‘INCATome/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘INCATome’ version ‘1.0’
* 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 ‘INCATome’ can be installed ... [45s/100s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/INCATome-00install.html' for details.
* checking package 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 ... [14s/46s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/31s] OK
* checking whether the package can be unloaded cleanly ... [13s/35s] OK
* checking whether the namespace can be loaded with stated dependencies ... [14s/33s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/34s] OK
* checking loading without being on the library search path ... [14s/35s] 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 ... [61s/142s] OK
* checking Rd files ... 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [30s/50s] OK
* checking PDF version of manual ... [7s/17s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘INCA_DEG combined table.txt’
  ‘INCA_DEG_LIMMA_significant_transEff.txt’
  ‘INCA_DEG_LIMMA_transEff.txt’ ‘INCA_DEG_LIMMA_volcano_transEff.jpg’
  ‘INCA_DEG_RP_transEff.txt’ ‘INCA_DEG_RP_transEff_significant.txt’
  ‘INCA_DEG_RP_volcano_transEff.jpg’
  ‘INCA_DEG_SAM_significant_transEff.txt’ ‘INCA_DEG_SAM_transEff.txt’
  ‘INCA_DEG_SAM_volcano_transEff.jpg’
  ‘INCA_DEG_TTEST_significant_transEff.txt’
  ‘INCA_DEG_TTEST_transEff.txt’ ‘INCA_DEG_TTEST_volcano_transEff.jpg’
  ‘MAplot1.jpg’ ‘MAplot10.jpg’ ‘MAplot11.jpg’ ‘MAplot12.jpg’
  ‘MAplot2.jpg’ ‘MAplot3.jpg’ ‘MAplot4.jpg’ ‘MAplot5.jpg’ ‘MAplot6.jpg’
  ‘MAplot7.jpg’ ‘MAplot8.jpg’ ‘MAplot9.jpg’
  ‘MAplot_post-INCANormIC_1.jpg’ ‘MAplot_post-INCANormIC_10.jpg’
  ‘MAplot_post-INCANormIC_11.jpg’ ‘MAplot_post-INCANormIC_12.jpg’
  ‘MAplot_post-INCANormIC_2.jpg’ ‘MAplot_post-INCANormIC_3.jpg’
  ‘MAplot_post-INCANormIC_4.jpg’ ‘MAplot_post-INCANormIC_5.jpg’
  ‘MAplot_post-INCANormIC_6.jpg’ ‘MAplot_post-INCANormIC_7.jpg’
  ‘MAplot_post-INCANormIC_8.jpg’ ‘MAplot_post-INCANormIC_9.jpg’
  ‘MAplot_post-INCANormSI_1.jpg’ ‘MAplot_post-INCANormSI_10.jpg’
  ‘MAplot_post-INCANormSI_11.jpg’ ‘MAplot_post-INCANormSI_12.jpg’
  ‘MAplot_post-INCANormSI_2.jpg’ ‘MAplot_post-INCANormSI_3.jpg’
  ‘MAplot_post-INCANormSI_4.jpg’ ‘MAplot_post-INCANormSI_5.jpg’
  ‘MAplot_post-INCANormSI_6.jpg’ ‘MAplot_post-INCANormSI_7.jpg’
  ‘MAplot_post-INCANormSI_8.jpg’ ‘MAplot_post-INCANormSI_9.jpg’
  ‘MAplot_pre-INCANormIC_1.jpg’ ‘MAplot_pre-INCANormIC_10.jpg’
  ‘MAplot_pre-INCANormIC_11.jpg’ ‘MAplot_pre-INCANormIC_12.jpg’
  ‘MAplot_pre-INCANormIC_2.jpg’ ‘MAplot_pre-INCANormIC_3.jpg’
  ‘MAplot_pre-INCANormIC_4.jpg’ ‘MAplot_pre-INCANormIC_5.jpg’
  ‘MAplot_pre-INCANormIC_6.jpg’ ‘MAplot_pre-INCANormIC_7.jpg’
  ‘MAplot_pre-INCANormIC_8.jpg’ ‘MAplot_pre-INCANormIC_9.jpg’
  ‘MAplot_pre-INCANormSI_1.jpg’ ‘MAplot_pre-INCANormSI_10.jpg’
  ‘MAplot_pre-INCANormSI_11.jpg’ ‘MAplot_pre-INCANormSI_12.jpg’
  ‘MAplot_pre-INCANormSI_2.jpg’ ‘MAplot_pre-INCANormSI_3.jpg’
  ‘MAplot_pre-INCANormSI_4.jpg’ ‘MAplot_pre-INCANormSI_5.jpg’
  ‘MAplot_pre-INCANormSI_6.jpg’ ‘MAplot_pre-INCANormSI_7.jpg’
  ‘MAplot_pre-INCANormSI_8.jpg’ ‘MAplot_pre-INCANormSI_9.jpg’
  ‘SpikeInPlot1.jpg’ ‘SpikeInPlot10.jpg’ ‘SpikeInPlot11.jpg’
  ‘SpikeInPlot12.jpg’ ‘SpikeInPlot2.jpg’ ‘SpikeInPlot3.jpg’
  ‘SpikeInPlot4.jpg’ ‘SpikeInPlot5.jpg’ ‘SpikeInPlot6.jpg’
  ‘SpikeInPlot7.jpg’ ‘SpikeInPlot8.jpg’ ‘SpikeInPlot9.jpg’
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 NOTE