* using log directory ‘/srv/hornik/tmp/CRAN_pretest/Sphinx.Rcheck’
* using R Under development (unstable) (2026-04-23 r89955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (3+b1)
    Debian flang version 21.1.8 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-04-24 07:23:10 UTC
* checking for file ‘Sphinx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Sphinx’ version ‘1.0.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/6s] NOTE
Maintainer: ‘Mengyi Yan <mongi126@163.com>’

New submission

Possibly misspelled words in DESCRIPTION:
  Proteomics (3:16)
  proteomics (8:50)

Size of tarball: 34029264 bytes
* 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 ‘Sphinx’ can be installed ... [17s/17s] 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [5s/5s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the package can be unloaded cleanly ... [5s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/5s] OK
* checking loading without being on the library search path ... [5s/5s] OK
* checking whether startup messages can be suppressed ... [5s/5s] 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 ... [23s/23s] 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 files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘01_spatial_distribution_celltype.jpg’ ‘02_distance_heatmap.jpg’
  ‘04_neighborhood_purity.jpg’ ‘05_spatial_distribution_clusters.jpg’
  ‘07_cluster_composition_barplot.jpg’ ‘08_interaction_heatmap.jpg’
  ‘10_spatial_network.jpg’ ‘11_cell_interaction_network.jpg’
  ‘12_voronoi_neighborhood.png’ ‘VolcanoPlots_AllClusters.png’
  ‘allmarker.jpg’ ‘annotation.Rmd’ ‘annotation.html’ ‘bar_plot.jpg’
  ‘bubble_plot.jpg’ ‘celltype_spatial_plot.png’ ‘codex_umap.jpg’
  ‘elbow_plot.png’ ‘functional.Rmd’ ‘functional.html’ ‘index.html’
  ‘installation.Rmd’ ‘installation.html’ ‘marker_heatmap.png’
  ‘preprocessing.Rmd’ ‘preprocessing.html’ ‘spatial-network.Rmd’
  ‘spatial-network.html’ ‘spatial_markers.png’ ‘umap_by_celltype.jpg’
  ‘umap_markers_plot.png’ ‘workflow.Rmd’ ‘workflow.html’ ‘workflow.png’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... [7s/7s] OK
* checking package vignettes ... NOTE
Package has ‘vignettes’ subdirectory but apparently no vignettes.
Perhaps the ‘VignetteBuilder’ information is missing from the
DESCRIPTION file?
* checking PDF version of manual ... [3s/3s] 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: 1 WARNING, 2 NOTEs