* using log directory 'd:/RCompile/CRANincoming/R-devel/scregclust.Rcheck'
* using R Under development (unstable) (2024-11-14 r87333 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'scregclust/DESCRIPTION' ... OK
* this is package 'scregclust' version '0.1.10'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [11s] NOTE
Maintainer: 'Felix Held <felix.held@gmail.com>'

New submission

Possibly misspelled words in DESCRIPTION:
  Larsson (13:14)
  al (13:32)
  et (13:29)
  scregclust (12:61)

Unknown, possibly misspelled, fields in DESCRIPTION:
  'Remotes'

Package has a VignetteBuilder field but no prebuilt vignette index.

Found the following (possibly) invalid URLs:
  URL: https://github.com/sven-nelander/scregclust/raw/main/datasets/pbmc_scregclust.rds (moved to https://github.com/scmethods/scregclust/raw/main/datasets/pbmc_scregclust.rds)
    From: inst/doc/pbmc.html
    Status: 301
    Message: Moved Permanently
  URL: https://scmethods.github.io/scregclust (moved to https://scmethods.github.io/scregclust/)
    From: README.md
    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.

The Title field should be in title case. Current version is:
  'Reconstructing the regulatory programs of target genes in single cell data'
In title case that is:
  'Reconstructing the Regulatory Programs of Target Genes in Single Cell Data'

The Description field should not start with the package name,
  'This package' or similar.
* 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 'scregclust' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 13.3.0'
* checking installed package size ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [11s] OK
* checking Rd files ... 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:
  plot_module_count_helper.Rd: ggplot2
  plot_silhouettes.Rd: ggplot2
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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... OK
  Running 'testthat.R'
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [57s] OK
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 2 NOTEs