* using log directory 'd:/RCompile/CRANincoming/R-devel/hicream.Rcheck'
* using R Under development (unstable) (2025-07-07 r88391 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 'hicream/DESCRIPTION' ... OK
* this is package 'hicream' version '0.0.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [48s] NOTE
Maintainer: 'Elise Jorge <elise.jorge@inrae.fr>'

New submission

Possibly misspelled words in DESCRIPTION:
  HIC (2:8)
  diffeREntial (2:12)

Found the following (possibly) invalid URLs:
  URL: https://www.gnu.org/software/gawk/
    From: inst/doc/A-Installation.html
    Status: Error
    Message: Timeout was reached [www.gnu.org]:
      Failed to connect to www.gnu.org port 443 after 21036 ms: Could not connect to server
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'hicream' 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 ... 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 ... [12s] OK
* checking whether the package can be loaded with stated dependencies ... [11s] OK
* checking whether the package can be unloaded cleanly ... [13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [13s] NOTE
Warning in check_forbidden_install("Python packages") :
  cannot install Python packages during R CMD check
Warning in check_forbidden_install("Python packages") :
  cannot install Python packages during R CMD check
Using virtual environment "hicreamvenv" ...
Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (1.7.0)
Requirement already satisfied: numpy>=1.22.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (2.3.1)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.16.0)
Requirement already satisfied: joblib>=1.2.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (3.6.0)

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... [11s] OK
* checking loading without being on the library search path ... [13s] OK
* checking whether startup messages can be suppressed ... [13s] NOTE
Using virtual environment "hicreamvenv" ...
+ "C:\Users\CRAN\Documents/.virtualenvs/hicreamvenv/Scripts/python.exe" -m pip install --upgrade --no-user scikit-learn
Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (1.7.0)
Requirement already satisfied: numpy>=1.22.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (2.3.1)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.16.0)
Requirement already satisfied: joblib>=1.2.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (3.6.0)

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (1.7.0)
Requirement already satisfied: numpy>=1.22.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (2.3.1)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.16.0)
Requirement already satisfied: joblib>=1.2.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (3.6.0)
* checking S3 generic/method consistency ... WARNING
Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (1.7.0)
Requirement already satisfied: numpy>=1.22.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (2.3.1)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.16.0)
Requirement already satisfied: joblib>=1.2.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (3.6.0)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* checking replacement functions ... WARNING
Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (1.7.0)
Requirement already satisfied: numpy>=1.22.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (2.3.1)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.16.0)
Requirement already satisfied: joblib>=1.2.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (3.6.0)
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... NOTE
Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (1.7.0)
Requirement already satisfied: numpy>=1.22.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (2.3.1)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.16.0)
Requirement already satisfied: joblib>=1.2.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (3.6.0)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... [52s] NOTE
Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (1.7.0)
Requirement already satisfied: numpy>=1.22.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (2.3.1)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.16.0)
Requirement already satisfied: joblib>=1.2.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (3.6.0)
Using virtual environment "hicreamvenv" ...
Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (1.7.0)
Requirement already satisfied: numpy>=1.22.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (2.3.1)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.16.0)
Requirement already satisfied: joblib>=1.2.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (3.6.0)

Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (1.7.0)
Requirement already satisfied: numpy>=1.22.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (2.3.1)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.16.0)
Requirement already satisfied: joblib>=1.2.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (3.6.0)
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (1.7.0)
Requirement already satisfied: numpy>=1.22.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (2.3.1)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.16.0)
Requirement already satisfied: joblib>=1.2.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (3.6.0)
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (1.7.0)
Requirement already satisfied: numpy>=1.22.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (2.3.1)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.16.0)
Requirement already satisfied: joblib>=1.2.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (3.6.0)
Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (1.7.0)
Requirement already satisfied: numpy>=1.22.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (2.3.1)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.16.0)
Requirement already satisfied: joblib>=1.2.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (3.6.0)
Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (1.7.0)
Requirement already satisfied: numpy>=1.22.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (2.3.1)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.16.0)
Requirement already satisfied: joblib>=1.2.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (3.6.0)
* checking Rd \usage sections ... NOTE
Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (1.7.0)
Requirement already satisfied: numpy>=1.22.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (2.3.1)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.16.0)
Requirement already satisfied: joblib>=1.2.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (1.5.1)
Requirement already satisfied: threadpoolctl>=3.1.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn) (3.6.0)
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [21s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [18s] OK
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 4 WARNINGs, 7 NOTEs