* using log directory ‘/srv/hornik/tmp/CRAN/PhyInsight.Rcheck’
* using R Under development (unstable) (2023-12-07 r85661)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.5 (1)
    Debian flang-new version 17.0.5 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘PhyInsight/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhyInsight’ version ‘0.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘James Churchward <jameschurchward1@outlook.com>’

New submission

Package has a VignetteBuilder field but no prebuilt vignette index.

The Description field contains
  (http://v4.boldsystems.org/index.php/api_home).
Please enclose URLs in angle brackets (<...>).
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘PhyInsight’ can be installed ... [1s/1s] 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [2s/2s] OK
* checking Rd files ... [0s/0s] 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 files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘PhyloTree_vignette_1.Rmd’ ‘PhyloTree_vignette_2.Rmd’
* checking examples ... [10s/27s] ERROR
Running examples in ‘PhyInsight-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: savePhytree
> ### Title: Save a Phylogenetic Tree Object
> ### Aliases: savePhytree
> 
> ### ** Examples
> 
> # create and plot a phylo tree
> specdf_Anth <- querySpecData("Antheraea polyphemus")[1:10,]
> 
> DNABin_Anth <- genDNABin(specdf_Anth)
> 
> DNAStringset_Anth <- genDNAStringSet(DNABin_Anth)
> 
> DNAStringSet_Anth_manipulated <- ManipStringSet(DNAStringset_Anth)
========================================================================================================================================================================================================

Time difference of 0.01 secs
Determining distance matrix based on shared 9-mers:
================================================================================

Time difference of 0 secs

Clustering into groups by similarity:
================================================================================

Time difference of 0 secs

Aligning Sequences:
================================================================================

Time difference of 0.03 secs

Iteration 1 of 2:

Determining distance matrix based on alignment:
================================================================================

Time difference of 0 secs

Reclustering into groups by similarity:
================================================================================

Time difference of 0 secs

Realigning Sequences:
================================================================================

Time difference of 0.03 secs

Alignment converged - skipping remaining iteration.

> 
> Phytree_Anth <- genPhytree(DNAStringSet_Anth_manipulated)
> 
> savePhytree(Phytree_Anth, specdf_Anth, "Anth_phylo_tree", 0.000055)
Error in withr::with_par(mar = c(0, 0, 0, 0)) : 
  unused argument (mar = c(0, 0, 0, 0))
Calls: savePhytree
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Directory 'inst/doc' does not exist.
Package vignettes without corresponding single PDF/HTML:
  ‘PhyloTree_vignette_1.Rmd’
  ‘PhyloTree_vignette_2.Rmd’
* checking re-building of vignette outputs ... [16s/34s] OK
* checking PDF version of manual ... [3s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... NOTE
Found the following files/directories:
  ‘Anth_phylo_tree’ ‘new_DNAString_file.fasta’
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 2 NOTEs