* using log directory 'd:/RCompile/CRANincoming/R-devel/Rato.Rcheck'
* using R Under development (unstable) (2025-06-02 r88257 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'Rato/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rato' version '0.1.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... WARNING
Maintainer: 'Victor Chavauty <lesserfish@pm.me>, Debora Guerra Peixe <deboraguerrapeixe@gmail.com>, Gabriel Piedade <gabrielpspiedade@gmail.com>'

The maintainer field is invalid or specifies more than one person

New submission

Non-FOSS package license (To do)

Possibly misspelled words in DESCRIPTION:
  RATO (3:37)

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Victor",
                    family = "Chavauty",
                    role = c("aut", "cre"),
                    email = "gabrielpspiedade@gmail.com")
as necessary.

Found the following (possibly) invalid URLs:
  URL: https://github.com/lesserfish/Rato/blob/main/manual.pdf
    From: README.md
    Status: 404
    Message: Not Found
* 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 hidden files and directories ... NOTE
Found the following hidden files and directories:
  .Rd2pdf81034
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.

CRAN-pack does not know about
  .Rd2pdf81034
* checking for portable file names ... WARNING
Found the following files with non-portable file names:
  Demos/IL17/Dynamics of the system after perturbation - Animation 2 - Constant Edges.R
  Demos/IL17/Dynamics of the system after perturbation - Animation.R
  Demos/IL17/Evolution of the System over Node Perturbations - Single Run - Fast.R
  Demos/IL17/Overall expression of System over Node Perturbations - Multiple runs - Fast.R
  Demos/IL17/Overall expression of System over Node Perturbations - Multiple runs - Slow.R
  Demos/IL17/Overall expression of System over Node Perturbations - Single runs - Slow.R
  Demos/IL17/Score of a gene inside a network.R
These are not fully portable file names.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking serialization versions ... OK
* checking whether package 'Rato' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
  To do
Standardizable: FALSE
* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  'Demos' 'Rato_Application_1.ipynb' 'build.r' 'manual.pdf' 'startup.R'
  'test.r'
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Found the following directory with the name of a Rd2pdf directory:
  ./.Rd2pdf81034
Most likely, these were included erroneously.
* 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 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 ... NOTE
graph.from.csv: no visible global function definition for 'read.csv'
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in Rd file 'graph.from.csv.Rd'
  '...'

Undocumented arguments in Rd file 'node.removal.thread.Rd'
  '...'
Documented arguments not in \usage in Rd file 'node.removal.thread.Rd':
  'times' 'to.numeric' 'only.final.state'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... NONE
* checking PDF version of manual ... [27s] OK
* checking HTML version of manual ... OK
* checking for code which exercises the package ... WARNING
No examples, no tests, no vignettes
* DONE
Status: 5 WARNINGs, 4 NOTEs