* using log directory 'd:/RCompile/CRANincoming/R-devel/Rtapas.Rcheck'
* using R Under development (unstable) (2024-06-03 r86679 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'Rtapas/DESCRIPTION' ... OK
* this is package 'Rtapas' version '1.2'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Mar Llaberia-Robledillo <mar.llaberia@uv.es>'

New submission

Package was archived on CRAN

Possibly misspelled words in DESCRIPTION:
  Llaberia (14:18)
  Robledillo (14:27)
  Tanglegram (2:15)
  al (14:41)
  et (14:38)
  phylogenetic (11:79)
  tanglegrams (10:66)

CRAN repository db overrides:
  X-CRAN-Comment: Archived on 2024-03-18 for policy violation.

  Attempting to use a cluster of 8 CPUs.
* 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 'Rtapas' can be installed ... 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 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 ... [15s] 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in 'Rtapas-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assoc_mat
> ### Title: Create an host-symbiont association matrix
> ### Aliases: assoc_mat
> 
> ### ** Examples
> 
> # data(nuc_cp)
> # NTaxa <- sort(NUCtr$tip.label)
> # CPTaxa <- sort(CPtr$tip.label)
> 
> NC <- assoc_mat(data.frame(NTaxa, CPTaxa))
Error: object 'NTaxa' not found
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... OK
  Running 'testthat.R'
* checking PDF version of manual ... [21s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE