* using log directory 'd:/RCompile/CRANincoming/R-devel/hicream.Rcheck'
* using R Under development (unstable) (2025-07-02 r88374 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 ... NOTE
Maintainer: 'Elise Jorge <elise.jorge@inrae.fr>'

New submission

Possibly misspelled words in DESCRIPTION:
  HIC (2:8)
  diffeREntial (2:12)
* 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 ... [15s] OK
* checking whether the package can be loaded with stated dependencies ... [14s] OK
* checking whether the package can be unloaded cleanly ... [15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [15s] OK
* checking whether the namespace can be unloaded cleanly ... [15s] OK
* checking loading without being on the library search path ... [15s] OK
* checking whether startup messages can be suppressed ... [16s] 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 ... [63s] OK
* 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 ... 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 data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [292s] ERROR
Running examples in 'hicream-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AggloClust2D
> ### Title: Performs constrained 2D agglomerative clustering
> ### Aliases: AggloClust2D print.res2D summary.res2D plot.res2D
> 
> ### ** Examples
> 
> data("pighic")
> res2D <- AggloClust2D(pighic$data)
Warning in check_forbidden_install("Python Virtual Environments") :
  cannot install Python Virtual Environments during R CMD check
Using Python: C:/Users/CRAN/AppData/Local/r-reticulate/r-reticulate/pyenv/pyenv-win/versions/3.11.9/python.exe
Creating virtual environment "hicreamvenv" ... 
+ "C:/Users/CRAN/AppData/Local/r-reticulate/r-reticulate/pyenv/pyenv-win/versions/3.11.9/python.exe" -m venv "C:\Users\CRAN\Documents/.virtualenvs/hicreamvenv"
Done!
Installing packages: pip, wheel, setuptools
+ "C:\Users\CRAN\Documents/.virtualenvs/hicreamvenv/Scripts/python.exe" -m pip install --upgrade pip wheel setuptools
Requirement already satisfied: pip in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (24.0)
Collecting pip
  Using cached pip-25.1.1-py3-none-any.whl.metadata (3.6 kB)
Collecting wheel
  Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Requirement already satisfied: setuptools in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (65.5.0)
Collecting setuptools
  Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 kB)
Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
  Attempting uninstall: pip
    Found existing installation: pip 24.0
    Uninstalling pip-24.0:
      Successfully uninstalled pip-24.0
Successfully installed pip-25.1.1 setuptools-80.9.0 wheel-0.45.1
Virtual environment 'hicreamvenv' successfully created.
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" ...
+ "C:\Users\CRAN\Documents/.virtualenvs/hicreamvenv/Scripts/python.exe" -m pip install --upgrade --no-user scikit-learn
Collecting scikit-learn
  Downloading scikit_learn-1.7.0-cp311-cp311-win_amd64.whl.metadata (14 kB)
Collecting numpy>=1.22.0 (from scikit-learn)
  Using cached numpy-2.3.1-cp311-cp311-win_amd64.whl.metadata (60 kB)
Collecting scipy>=1.8.0 (from scikit-learn)
  Using cached scipy-1.16.0-cp311-cp311-win_amd64.whl.metadata (60 kB)
Collecting joblib>=1.2.0 (from scikit-learn)
  Downloading joblib-1.5.1-py3-none-any.whl.metadata (5.6 kB)
Collecting threadpoolctl>=3.1.0 (from scikit-learn)
  Downloading threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
Downloading scikit_learn-1.7.0-cp311-cp311-win_amd64.whl (10.7 MB)
   ---------------------------------------- 10.7/10.7 MB 27.9 MB/s eta 0:00:00
Downloading joblib-1.5.1-py3-none-any.whl (307 kB)
Using cached numpy-2.3.1-cp311-cp311-win_amd64.whl (13.0 MB)
Using cached scipy-1.16.0-cp311-cp311-win_amd64.whl (38.6 MB)
Downloading threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
Installing collected packages: threadpoolctl, numpy, joblib, scipy, scikit-learn

Successfully installed joblib-1.5.1 numpy-2.3.1 scikit-learn-1.7.0 scipy-1.16.0 threadpoolctl-3.6.0
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" ...
+ "C:\Users\CRAN\Documents/.virtualenvs/hicreamvenv/Scripts/python.exe" -m pip install --upgrade --no-user kneebow
Collecting kneebow
  Downloading kneebow-1.0.2.tar.gz (4.5 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: numpy in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from kneebow) (2.3.1)
Collecting matplotlib (from kneebow)
  Using cached matplotlib-3.10.3-cp311-cp311-win_amd64.whl.metadata (11 kB)
Requirement already satisfied: scikit-learn in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from kneebow) (1.7.0)
Collecting contourpy>=1.0.1 (from matplotlib->kneebow)
  Using cached contourpy-1.3.2-cp311-cp311-win_amd64.whl.metadata (5.5 kB)
Collecting cycler>=0.10 (from matplotlib->kneebow)
  Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting fonttools>=4.22.0 (from matplotlib->kneebow)
  Using cached fonttools-4.58.4-cp311-cp311-win_amd64.whl.metadata (108 kB)
Collecting kiwisolver>=1.3.1 (from matplotlib->kneebow)
  Using cached kiwisolver-1.4.8-cp311-cp311-win_amd64.whl.metadata (6.3 kB)
Collecting packaging>=20.0 (from matplotlib->kneebow)
  Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Collecting pillow>=8 (from matplotlib->kneebow)
  Downloading pillow-11.3.0-cp311-cp311-win_amd64.whl.metadata (9.2 kB)
Collecting pyparsing>=2.3.1 (from matplotlib->kneebow)
  Using cached pyparsing-3.2.3-py3-none-any.whl.metadata (5.0 kB)
Collecting python-dateutil>=2.7 (from matplotlib->kneebow)
  Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting six>=1.5 (from python-dateutil>=2.7->matplotlib->kneebow)
  Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Requirement already satisfied: scipy>=1.8.0 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from scikit-learn->kneebow) (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->kneebow) (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->kneebow) (3.6.0)
Using cached matplotlib-3.10.3-cp311-cp311-win_amd64.whl (8.1 MB)
Using cached contourpy-1.3.2-cp311-cp311-win_amd64.whl (222 kB)
Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB)
Using cached fonttools-4.58.4-cp311-cp311-win_amd64.whl (2.2 MB)
Using cached kiwisolver-1.4.8-cp311-cp311-win_amd64.whl (71 kB)
Using cached packaging-25.0-py3-none-any.whl (66 kB)
Downloading pillow-11.3.0-cp311-cp311-win_amd64.whl (7.0 MB)
   ---------------------------------------- 7.0/7.0 MB 28.6 MB/s eta 0:00:00
Using cached pyparsing-3.2.3-py3-none-any.whl (111 kB)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Building wheels for collected packages: kneebow
  DEPRECATION: Building 'kneebow' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'kneebow'. Discussion can be found at https://github.com/pypa/pip/issues/6334
  Building wheel for kneebow (setup.py): started
  Building wheel for kneebow (setup.py): finished with status 'done'
  Created wheel for kneebow: filename=kneebow-1.0.2-py3-none-any.whl size=4843 sha256=741b71be9f5e3262e06f7f3a5b20d027103bb688d41e0d1063c4cfeaa08befd7
  Stored in directory: c:\users\cran\appdata\local\pip\cache\wheels\e1\7c\fa\78caeaa5e66eb8b04f01b836232b357da6663811c04939e53f
Successfully built kneebow
Installing collected packages: six, pyparsing, pillow, packaging, kiwisolver, fonttools, cycler, contourpy, python-dateutil, matplotlib, kneebow

Successfully installed contourpy-1.3.2 cycler-0.12.1 fonttools-4.58.4 kiwisolver-1.4.8 kneebow-1.0.2 matplotlib-3.10.3 packaging-25.0 pillow-11.3.0 pyparsing-3.2.3 python-dateutil-2.9.0.post0 six-1.17.0
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" ...
+ "C:\Users\CRAN\Documents/.virtualenvs/hicreamvenv/Scripts/python.exe" -m pip install --upgrade --no-user pandas
Collecting pandas
  Using cached pandas-2.3.0-cp311-cp311-win_amd64.whl.metadata (19 kB)
Requirement already satisfied: numpy>=1.23.2 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from pandas) (2.3.1)
Requirement already satisfied: python-dateutil>=2.8.2 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from pandas) (2.9.0.post0)
Collecting pytz>=2020.1 (from pandas)
  Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas)
  Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
Requirement already satisfied: six>=1.5 in c:\users\cran\docume~1\virtua~1\hicrea~1\lib\site-packages (from python-dateutil>=2.8.2->pandas) (1.17.0)
Using cached pandas-2.3.0-cp311-cp311-win_amd64.whl (11.1 MB)
Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
Installing collected packages: pytz, tzdata, pandas

Successfully installed pandas-2.3.0 pytz-2025.2 tzdata-2025.2
Error: Required version of NumPy not available: installation of Numpy >= 1.6 not found
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [26s] OK
* checking PDF version of manual ... [20s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE