* using log directory 'd:/RCompile/CRANincoming/R-devel/jrSiCKLSNMF.Rcheck'
* using R Under development (unstable) (2025-02-11 r87713 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 'jrSiCKLSNMF/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'jrSiCKLSNMF' version '1.2.2'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [78s] NOTE
Maintainer: 'Dorothy Ellis <ddemoreellis@gmail.com>'

Possibly misspelled words in DESCRIPTION:
  Datta (12:718)
  Dimensionality (3:37)
  Kullback (12:69)
  Leibler (12:78)
  Multimodal (3:8)
  NMF (12:170)
  Omics (3:31)
  multimodal (12:210)
  omics (12:221, 12:411)
  pre (12:523)
  scATAC (12:302)
  scRNA (12:288)

Found the following (possibly) invalid DOIs:
  DOI: 10.1007/978-3-642-04180-8_45/COVER
    From: man/RunjrSiCKLSNMF.Rd
          man/jrSiCKLSNMF.Rd
    Status: 404
    Message: Not Found
  DOI: 10.1186/1471-2105-11-367/FIGURES/5
    From: man/GenerateWmatricesandHmatrix.Rd
    Status: 404
    Message: Not Found
  DOI: 10.12688/F1000RESEARCH.9501.2/DOI
    From: man/BuildKNNGraphLaplacians.Rd
          man/BuildSNNGraphLaplacians.Rd
          man/ClusterSickleJr.Rd
    Status: 404
    Message: Not Found
* 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 'jrSiCKLSNMF' 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 '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 ... [12s] OK
* checking whether the package can be loaded with stated dependencies ... [10s] OK
* checking whether the package can be unloaded cleanly ... [12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s] OK
* checking whether the namespace can be unloaded cleanly ... [12s] OK
* checking loading without being on the library search path ... [12s] 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 ... [50s] OK
* checking Rd files ... [13s] 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:
  PlotSickleJrUMAP.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 ... WARNING
Error: package or namespace load failed for 'jrSiCKLSNMF' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'ggrepel'
Call sequence:
6: stop(msg, call. = FALSE, domain = NA)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
       attr(package, "LibPath") <- which.lib.loc
       ns <- loadNamespace(package, lib.loc)
       env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)
   }, error = function(e) {
       P <- if (!is.null(cc <- conditionCall(e))) 
           paste(" in", deparse(cc)[1L])
       else ""
       msg <- gettextf("package or namespace load failed for %s%s:\n %s", 
           sQuote(package), P, conditionMessage(e))
       if (logical.return && !quietly) 
           message(paste("Error:", msg), domain = NA)
       else stop(msg, call. = FALSE, domain = NA)
   })
1: library(package, lib.loc = lib.loc, charac
Execution halted
* checking Rd \usage sections ... NOTE
Error: there is no package called 'ggrepel'
Call sequence:
9: doWithOneRestart(return(expr), restart)
8: withOneRestart(expr, restarts[[1L]])
7: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
5: asNamespace(ns)
4: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
3: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
2: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
1: loadNamespace(package, lib.loc)
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... [13s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 ... [27s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [215s] OK
* checking PDF version of manual ... [25s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 WARNING, 3 NOTEs