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RobLoxBioC log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2024-02-11-11-44/RF_PKG_CHECK/PKGS/RobLoxBioC.Rcheck'
* using R version 4.3.2 Patched (2024-02-08 r85879 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows 10 x64 (build 19045)
* using session charset: UTF-8
* using option '--as-cran'
* checking for file 'RobLoxBioC/DESCRIPTION' ... OK
* this is package 'RobLoxBioC' version '1.2.2'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Matthias Kohl '

New submission

Package was archived on CRAN

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2024-01-13 as requires archived package
    'RobLox'.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'
* 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 serialization versions ... OK
* checking whether package 'RobLoxBioC' can be installed ... [24s] OK
* 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 R 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 ... [33s] OK
* checking Rd files ... 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [11s] OK
* checking examples with --run-donttest ... ERROR
Running examples in 'RobLoxBioC-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: KolmogorovMinDist
> ### Title: Generic Function for Computing Minimum Kolmogorov Distance for
> ###   Biological Data
> ### Aliases: KolmogorovMinDist KolmogorovMinDist-methods
> ###   KolmogorovMinDist,matrix,Norm-method
> ###   KolmogorovMinDist,AffyBatch,AbscontDistribution-method
> ###   KolmogorovMinDist,beadLevelData,AbscontDistribution-method
> ### Keywords: robust
> 
> ### ** Examples
> 
> set.seed(123) # to have reproducible results for package checking
> 
> ## matrix method for KolmogorovMinDist
> ind <- rbinom(200, size=1, prob=0.05) 
> X <- matrix(rnorm(200, mean=ind*3, sd=(1-ind) + ind*9), nrow = 2)
> KolmogorovMinDist(X, D = Norm())
$dist
[1] 0.06544843 0.04356402

$n
[1] 100 100

> 
> ## using Affymetrix data
> data(SpikeIn)
> probes <- log2(pm(SpikeIn))
> (res <- KolmogorovMinDist(probes, Norm()))
$dist
 [1] 0.1755693 0.1567648 0.1571403 0.1609188 0.1617499 0.1607157 0.1382646
 [8] 0.1471997 0.1693088 0.1836652 0.1787724 0.1601283 0.1729001 0.1519412
[15] 0.1682097 0.1662173 0.1547481 0.1716497 0.1751219 0.1671566

$n
 [1] 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12

> boxplot(res$dist)
> 
> ## No test: 
> ## \donttest because of check time
> ## using Affymetrix data
> library(affydata)
Error in library(affydata) : there is no package called 'affydata'
Execution halted
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  'R:/run/building/build_2024-02-11-11-44/RF_PKG_CHECK/PKGS/RobLoxBioC.Rcheck/00check.log'
for details.

Run time: 225.59 seconds.