* using log directory 'd:/RCompile/CRANincoming/R-devel/dartR.Rcheck'
* using R version 4.5.0 alpha (2025-03-24 r88048 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'dartR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dartR' version '2.9.9.5'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [12s] NOTE
Maintainer: 'Bernd Gruber <bernd.gruber@canberra.edu.au>'

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  heterozygosity (27:53)
  polymorphism (20:30)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2025-01-10 as issues were not corrected
    in time.
* 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 'dartR' can be installed ... OK
* 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 ... [12s] OK
* checking whether the package can be unloaded cleanly ... [12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s] OK
* checking whether the namespace can be unloaded cleanly ... [11s] OK
* checking loading without being on the library search path ... [13s] OK
* checking whether startup messages can be suppressed ... [11s] 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 ... [21s] NOTE
Error: there is no package called 'plyr'
Call sequence:
11: doWithOneRestart(return(expr), restart)
10: withOneRestart(expr, restarts[[1L]])
9: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
8: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
7: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
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(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
2: namespaceImport(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), 
       versionCheck = vI[[j]]), from = package, except = i$except)
1: loadNamespace(package, lib.loc)
Execution halted
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called 'plyr'
Calls: <Anonymous>
Execution halted

Error: there is no package called 'plyr'
Call sequence:
11: doWithOneRestart(return(expr), restart)
10: withOneRestart(expr, restarts[[1L]])
9: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
8: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
7: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
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(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
2: namespaceImport(ns, loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), 
       versionCheck = vI[[j]]), from = package, except = i$except)
1: loadNamespace(package, lib.loc)
Execution halted
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Error: package 'adegenet' could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)), 
       call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc, 
       .libPaths()))
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Error: package 'adegenet' could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)), 
       call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc, 
       .libPaths()))
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error: package 'adegenet' could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)), 
       call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc, 
       .libPaths()))
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
Error: package 'adegenet' could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)), 
       call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc, 
       .libPaths()))
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
* checking Rd \usage sections ... NOTE
Error: there is no package called 'later'
Call sequence:
14: doWithOneRestart(return(expr), restart)
13: withOneRestart(expr, restarts[[1L]])
12: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
11: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
10: asNamespace(ns)
9: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc, 
       .libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
8: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
7: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()), 
       versionCheck = vI[[i]]), from = package)
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(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
2: namespaceImport(ns, loadNamespace(j <- i[[1L]], 
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 ... WARNING
  Failed with error:  'there is no package called 'later''
  Error loading dataset 'bandicoot.gl':
   Error in .requirePackage(package) : 
    unable to load required package 'adegenet'
  
  Failed with error:  'there is no package called 'later''
  Error loading dataset 'possums.gl':
   Error in .requirePackage(package) : 
    unable to load required package 'adegenet'
  
  Failed with error:  'there is no package called 'later''
  Error loading dataset 'testset.gl':
   Error in .requirePackage(package) : 
    unable to load required package 'adegenet'
  
  Failed with error:  'there is no package called 'later''
  Error loading dataset 'testset.gs':
   Error in .requirePackage(package) : 
    unable to load required package 'adegenet'
  
  The dataset(s) may use package(s) not declared in Depends/Imports.
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'dartR-Ex.R' failed
The error occurred in:


R version 4.5.0 alpha (2025-03-24 r88048 ucrt)
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "dartR"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> base::assign(".ExTimings", "dartR-Ex.timings", pos = 'CheckExEnv')
> base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
> base::assign(".format_ptime",
+ function(x) {
+   if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
+   if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
+   options(OutDec = '.')
+   format(x[1L:3L], digits = 7L)
+ },
+ pos = 'CheckExEnv')
> 
> ### * </HEADER>
> library('dartR')
Loading required package: adegenet
Loading required package: ade4
Error: package or namespace load failed for 'adegenet' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'later'
Error: package 'adegenet' could not be loaded
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [36s] OK
* checking HTML version of manual ... [43s] OK
* DONE
Status: 1 ERROR, 3 WARNINGs, 3 NOTEs