* using log directory ‘/srv/hornik/tmp/CRAN_pretest/simone.Rcheck’
* using R Under development (unstable) (2026-02-19 r89439)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (1+b1)
    Debian flang version 21.1.8 (1+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-02-20 21:54:05 UTC
* checking for file ‘simone/DESCRIPTION’ ... OK
* this is package ‘simone’ version ‘1.0-5’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Christophe Ambroise <christophe.ambroise@univ-evry.fr>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  MOdular (4:34)
  NEtworks (4:42)
  SIMoNe (4:52)
  simone (22:34)
  transcriptomic (18:5)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2020-10-02 as check issues were not
    corrected in time.
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘simone’ can be installed ... [4s/4s] OK
* used C compiler: ‘Debian clang version 21.1.8 (3)’
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [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 ... NOTE
Mismatches for apparent methods not registered:
plot:
  function(x, ...)
plot.path:
  function(o, x.axis, main, ...)

plot:
  function(x, ...)
plot.sequence:
  function(o, main)

plot:
  function(x, ...)
plot.ROC:
  function(o, Theta.star, main, type, ...)

plot:
  function(x, ...)
plot.PR:
  function(o, Theta.star, main, type, ...)

plot:
  function(x, ...)
plot.BIC:
  function(o, main, ...)

plot:
  function(x, ...)
plot.AIC:
  function(o, main, ...)
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [8s/8s] 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in ‘demo’ ... NOTE
'library' or 'require' call not declared from: ‘glasso’
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] NOTE
Found the following HTML validation problems:
rTranscriptData.html:93:1 (rTranscriptData.Rd:58): Warning: <center> element removed from HTML5
rTranscriptData.html:113:1 (rTranscriptData.Rd:86): Warning: <center> element removed from HTML5
simone.html:105:1 (simone.Rd:70): Warning: inserting implicit <p>
simone.html:105:1 (simone.Rd:70): Warning: trimming empty <p>
simone.html:101:1 (simone.Rd:65): Warning: <center> element removed from HTML5
simone.html:134:1 (simone.Rd:104): Warning: <center> element removed from HTML5
simone.html:142:1 (simone.Rd:114): Warning: <center> element removed from HTML5
simone.html:1501:1 (simone.Rd:70): Warning: inserting implicit <p>
simone.html:1501:1 (simone.Rd:70): Warning: trimming empty <p>
simone.html:1098:1 (rTranscriptData.Rd:58): Warning: <center> element removed from HTML5
simone.html:1118:1 (rTranscriptData.Rd:86): Warning: <center> element removed from HTML5
simone.html:1497:1 (simone.Rd:65): Warning: <center> element removed from HTML5
simone.html:1530:1 (simone.Rd:104): Warning: <center> element removed from HTML5
simone.html:1538:1 (simone.Rd:114): Warning: <center> element removed from HTML5
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 4 NOTEs