* using log directory 'd:/RCompile/CRANincoming/R-devel/SuperCell.Rcheck'
* using R Under development (unstable) (2024-05-22 r86590 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'SuperCell/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SuperCell' version '1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'The package maintainer <leonard.herault@unil.ch>'

New submission

Non-FOSS package license (file LICENSE)

Possibly misspelled words in DESCRIPTION:
  metacell (8:53)
  scRNA (3:26)

Unknown, possibly misspelled, fields in DESCRIPTION:
  'Remotes'

Suggests or Enhances not in mainstream repositories:
  velocyto.R

Found the following (possibly) invalid URLs:
  URL: https://cloud.r-project.org/web/packages/ggplot2/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/Hmisc/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/Matrix/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/RANN/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/Seurat/index.html
    From: inst/doc/a_SuperCell.html
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/WeightedCluster/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/corpcor/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/igraph/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/irlba/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/patchwork/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/plyr/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.r-project.org/web/packages/weights/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://cran.rstudio.com/web/packages/matrixStats/index.html
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://dev.biologists.org/content/146/12/dev173849.abstract (moved to https://journals.biologists.com/dev/article/146/12/dev173849/19483/Comprehensive-single-cell-mRNA-profiling-reveals-a)
    From: man/pancreas.Rd
    Status: 301
    Message: Moved Permanently
  URL: https://doi:10.1101/gr.230771.117
    From: README.md
    Status: Error
    Message: URL rejected: Port number was not a decimal number between 0 and 65535
  URL: https://github.com/LuyiTian/sc_mixology/blob/master/data/ (moved to https://github.com/LuyiTian/sc_mixology/tree/master/data)
    From: inst/doc/a_SuperCell.html
    Status: 301
    Message: Moved Permanently
  URL: https://scvelo.readthedocs.io/Pancreas.html
    From: man/pancreas.Rd
    Status: 404
    Message: Not Found
  The canonical URL of the CRAN page for a package is 
    https://CRAN.R-project.org/package=pkgname
  Canonical CRAN.R-project.org URLs use https.
  For content that is 'Moved Permanently', please change http to https,
  add trailing slashes, or replace the old by the new URL.

The Title field should be in title case. Current version is:
'Simplification of scRNA-seq data by merging together similar cells'
In title case that is:
'Simplification of scRNA-Seq Data by Merging Together Similar Cells'

DESCRIPTION fields with placeholder content:
  Maintainer: The package maintainer <leonard.herault@unil.ch>

Size of tarball: 9406831 bytes

Found the following URLs which should use \doi (with the DOI name only):
  File 'cell_lines.Rd':
    https://doi.org/10.1038/s41592-019-0425-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'velocyto.R'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SuperCell' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  'plots'
* 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 whether startup messages can be suppressed ... 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 ... [11s] NOTE
supercell_2_Seurat: no visible global function definition for
  'packageVersion'
supercell_2_Seurat: no visible global function definition for 'as'
Undefined global functions or variables:
  as packageVersion
Consider adding
  importFrom("methods", "as")
  importFrom("utils", "packageVersion")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Unknown package 'velocyto.R' in Rd xrefs
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [13s] OK
  Running 'testthat.R' [13s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [92s] OK
* checking PDF version of manual ... [22s] OK
* checking HTML version of manual ... OK
* DONE
Status: 5 NOTEs