* using log directory ‘/srv/hornik/tmp/CRAN_pretest/lcc.Rcheck’
* using R Under development (unstable) (2025-11-22 r89050)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.5 (1)
    Debian flang version 21.1.5 (1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘lcc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lcc’ version ‘3.2.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/8s] NOTE
Maintainer: ‘Thiago de Paula Oliveira <thiago.paula.oliveira@alumni.usp.br>’

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  LCC (21:42)
  Oliveira (26:15)
  al (26:27)
  et (26:24)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2025-11-07 as issues were not corrected
    despite reminders.

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following (possibly) invalid URLs:
  URL: http://CRAN.R-project.org/doc/manuals/R-admin.pdf
    From: README.md
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: https://codecov.io/github/Prof-ThiagoOliveira/lcc?branch=master (moved to https://app.codecov.io/github/Prof-ThiagoOliveira/lcc?branch=master)
    From: README.md
    Status: 301
    Message: Moved Permanently
  URL: https://peerj.com/articles/9850.pdf
    From: README.md
    Status: 400
    Message: Bad Request
  URL: https://travis-ci.org/Prof-ThiagoOliveira/lcc (moved to https://app.travis-ci.com/Prof-ThiagoOliveira/lcc)
    From: README.md
    Status: 301
    Message: Moved Permanently
Canonical CRAN.R-project.org URLs use https.
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.
* 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 serialization versions ... OK
* checking whether package ‘lcc’ can be installed ... [4s/4s] OK
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [8s/8s] NOTE
CCC_lin : calculateCCC_fast: no visible global function definition for
  ‘reshape’
Pearson : calculateCorrelation_fast: no visible global function
  definition for ‘reshape’
plotBuilder_lpc: no visible global function definition for ‘clamp01’
Undefined global functions or variables:
  clamp01 reshape
Consider adding
  importFrom("stats", "reshape")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anova.lcc.Rd: anova.lme
  coef.lcc.Rd: nlme
  logLik.lcc.Rd: nlme
  print.anova.lcc.Rd: anova.lme, nlme
  ranef.lcc.Rd: nlme
  residuals.lcc.Rd: nlme
  vcov.lcc.Rd: nlme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [6s/6s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [21s/21s] OK
  Running ‘testthat.R’ [21s/21s]
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [2s/2s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 NOTEs