* using log directory ‘/srv/hornik/tmp/CRAN_pretest/LSAMBA.Rcheck’
* using R Under development (unstable) (2025-05-11 r88197)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3)
    Debian flang-new version 19.1.7 (3)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘LSAMBA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LSAMBA’ version ‘2024.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Auriane Gabaut <auriane.gabaut@inria.fr>’

New submission

Version contains large components (2024.1.0)

Possibly misspelled words in DESCRIPTION:
  Lavielle (17:172)

The Description field contains
  (M Prague, M Lavielle (2022) <https://doi.org/10.1002/psp4.12742>). The
Please write DOIs as <doi:prefix/suffix>.
* 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 ‘LSAMBA’ can be installed ... [4s/4s] WARNING
Found the following significant warnings:
  Note: possible error in 'Rsmlx.covariateModelSelection(pen.coef = pen.coef, ': unused argument (print = print) 
See ‘/srv/hornik/tmp/CRAN_pretest/LSAMBA.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 ... [6s/6s] NOTE
covariateModelSelection: possible error in
  Rsmlx.covariateModelSelection(pen.coef = pen.coef, nb.model =
  nb.model, weight = weight, covToTransform = NULL, covFix = covFix,
  direction = direction, steps = steps, p.max = p.max, paramToUse =
  paramToUse, sp0 = sp0, iter = iter, correlation.model =
  correlation.model, n.full = n.full, eta = eta, print = print): unused
  argument (print = print)
* 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 ... WARNING
Codoc mismatches from Rd file 'buildmlx.Rd':
buildmlx
  Code: function(project = NULL, final.project = NULL, model = "all",
                 prior = NULL, weight = NULL, coef.w1 = 0.5, paramToUse
                 = "all", covToTest = "all", covToTransform = "none",
                 center.covariate = FALSE, criterion = "BICc",
                 linearization = FALSE, ll = TRUE, test = FALSE,
                 direction = NULL, steps = 1000, n.full = 10, max.iter
                 = 20, explor.iter = 2, fError.min = 0.001, seq.cov =
                 FALSE, seq.cov.iter = 0, seq.corr = TRUE, p.max = if
                 (buildMethod == "stepAIC") { 0.1} else { 1}, p.min =
                 c(0.075, 0.05, 0.1), print = TRUE, nb.model = 1,
                 nfolds = 5, alpha = 1, nSS = 1000, buildMethod =
                 "lasso", FDR_thr = 0.1)
  Docs: function(project = NULL, final.project = NULL, model = "all",
                 prior = NULL, weight = NULL, coef.w1 = 0.5, paramToUse
                 = "all", covToTest = "all", covToTransform = "none",
                 center.covariate = FALSE, criterion = "BICc",
                 linearization = FALSE, ll = T, test = F, direction =
                 NULL, steps = 1000, n.full = 10, max.iter = 20,
                 explor.iter = 2, fError.min = 0.001, seq.cov = FALSE,
                 seq.cov.iter = 0, seq.corr = TRUE, p.max = if
                 (buildMethod == "stepAIC") { 0.1} else { 1}, p.min =
                 c(0.075, 0.05, 0.1), print = TRUE, nb.model = 1,
                 nfolds = 5, alpha = 1, nSS = 1000, buildMethod =
                 "lasso", FDR_thr = 0.1)
  Mismatches in argument default values:
    Name: 'll' Code: TRUE Docs: T
    Name: 'test' Code: FALSE Docs: F

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [1s/1s] OK
* checking PDF version of manual ... [2s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 WARNINGs, 2 NOTEs