* using log directory ‘/srv/hornik/tmp/CRAN/singleCellHaystack.Rcheck’
* using R Under development (unstable) (2024-01-10 r85799)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (3)
    Debian flang-new version 17.0.6 (3)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘singleCellHaystack/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellHaystack’ version ‘1.0.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] NOTE
Maintainer: ‘Alexis Vandenbon <alexis.vandenbon@gmail.com>’

Package has a VignetteBuilder field but no prebuilt vignette index.
* 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 serialization versions ... OK
* checking whether package ‘singleCellHaystack’ can be installed ... [5s/5s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [8s/8s] OK
* checking Rd files ... [0s/0s] 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 files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘a01_toy_example.Rmd’ ‘examples/a02_example_scRNAseq.Rmd’
  ‘examples/a03_example_spatial_visium.Rmd’
  ‘examples/a04_example_spatial_slideseqV2.Rmd’
  ‘examples/a05_moca_100k.Rmd’ ‘examples/a06_pseudotime.Rmd’
  ‘examples/a07_gene_sets.Rmd’ ‘examples/a08_gene_clustering.Rmd’
  ‘examples/a08_gene_clustering.nb.html’
  ‘examples/figures/a05-plot_dim-1.png’
  ‘examples/figures/a05-plot_results-1.png’
  ‘examples/figures/a06-plot_cells_1-1.png’
  ‘examples/figures/a06-plot_cells_2-1.png’
  ‘examples/figures/a06-plot_cells_2-2.png’
  ‘examples/figures/a06-plot_cells_3-1.png’
  ‘examples/figures/a06-plot_cells_4-1.png’
  ‘examples/figures/a06-plot_cells_5-1.png’
  ‘examples/figures/a06-plot_genes_1-1.png’
  ‘examples/figures/a06-plot_genes_2-1.png’
  ‘examples/figures/a06-plot_genes_2-2.png’
  ‘examples/figures/a06-plot_haystack_1-1.png’
  ‘examples/figures/a06-plot_haystack_1-2.png’
  ‘examples/figures/a06-plot_haystack_2-1.png’
  ‘examples/figures/a06-plot_haystack_3-1.png’
  ‘examples/figures/a06-plot_pca-1.png’
* checking examples ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [9s/9s] OK
  Running ‘testthat.R’ [9s/9s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... WARNING
Directory 'inst/doc' does not exist.
Package vignette without corresponding single PDF/HTML:
  ‘a01_toy_example.Rmd’
* checking re-building of vignette outputs ... [10s/10s] OK
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE