* using log directory ‘/srv/hornik/tmp/CRAN/SuperCell.Rcheck’
* using R Under development (unstable) (2024-06-30 r86854)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (1)
    Debian flang-new version 18.1.8 (1)
* running under: Debian GNU/Linux trixie/sid
* 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 ... [3s/4s] NOTE
Maintainer: ‘Leonard Herault <leonard.herault@unil.ch>’

New submission

Non-FOSS package license (file LICENSE)

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

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://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
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.

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’

Size of tarball: 9381733 bytes
* 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 executable files ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

CRAN-pack does not know about
  .github
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SuperCell’ can be installed ... [31s/31s] 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking whether startup messages can be suppressed ... [0s/0s] 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 ... [5s/5s] 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 ... [1s/1s] 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 ... [0s/0s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [6s/6s] OK
  Running ‘testthat.R’ [6s/6s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [110s/110s] OK
* 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: 4 NOTEs