* using log directory ‘/srv/hornik/tmp/CRAN_pretest/digitalDLSorteR.Rcheck’
* using R Under development (unstable) (2024-09-10 r87115)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘digitalDLSorteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘digitalDLSorteR’ version ‘1.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/10s] NOTE
Maintainer: ‘Diego Mañanes <dmananesc@cnic.es>’

Found the following (possibly) invalid URLs:
  URL: https://academic.oup.com/bioinformatics/article/40/2/btae072/7609037
    From: README.md
    Status: 403
    Message: Forbidden
  URL: https://keras.posit.co/articles/getting_started.html (moved to https://keras3.posit.co/articles/getting_started.html)
    From: inst/doc/kerasIssues.html
    Status: 301
    Message: Moved Permanently
For content that is 'Moved Permanently', please change http to https,
add trailing slashes, or replace the old by the new URL.

Size of tarball: 5524246 bytes
* 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 ‘digitalDLSorteR’ can be installed ... [23s/23s] 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] OK
* checking whether startup messages can be suppressed ... [6s/6s] 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 ... [31s/31s] OK
* 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:
  DigitalDLSorter-class.Rd: SingleCellExperiment-class,
    dgCMatrix-class, ZinbModel-class, SummarizedExperiment-class
  ZinbParametersModel-class.Rd: ZinbModel-class
  bulk.simul.Rd: SummarizedExperiment-class
  createDDLSobject.Rd: SingleCellExperiment-class,
    SummarizedExperiment-class
  loadDeconvData.Rd: SummarizedExperiment-class
  simSCProfiles.Rd: SingleCellExperiment-class
  single.cell.real.Rd: SingleCellExperiment-class
  single.cell.simul.Rd: SingleCellExperiment-class
  zinb.params.Rd: ZinbModel-class
  zinbwave.model.Rd: ZinbModel-class
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [22s/22s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [24s/24s] OK
  Running ‘testthat.R’ [24s/24s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [3s/3s] OK
* checking PDF version of manual ... [4s/4s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 NOTEs