* using log directory 'd:/RCompile/CRANincoming/R-devel/HybridMicrobiomes.Rcheck'
* using R Under development (unstable) (2023-11-30 r85651 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'HybridMicrobiomes/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HybridMicrobiomes' version '0.1.1'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Sharon Bewick <sbewick@clemson.edu>'

Possibly misspelled words in DESCRIPTION:
  barnett (27:542)
  david (27:536)
  davidbarnett (27:332)
  devtools (27:487, 27:510)
  getOption (27:387)
  github (27:528)
  microViz (27:180, 27:241, 27:311, 27:420, 27:550)
  repos (27:322, 27:398)

Suggests or Enhances not in mainstream repositories:
  microViz

The Description field contains
  "https://david-barnett.r-universe.dev", getOption("repos"))). To
Please enclose URLs in angle brackets (<...>).
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'microViz'
* 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 'HybridMicrobiomes' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... [25s] NOTE
FourHbootstrapA: no visible binding for global variable 'median'
FourHpreanalysis: no visible global function definition for 'median'
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'FourHbootstrap.Rd':
  \usage lines wider than 90 characters:
     FourHbootstrap(x, class_grouping, core_fraction, boot_no, sample_no, core_average_abundance = 0, core_max_abundance = 0, core_all_avera ... [TRUNCATED]

Rd file 'FourHbootstrapA.Rd':
  \usage lines wider than 90 characters:
     FourHbootstrapA(x, class_grouping, core_fraction, boot_no, sample_no, core_average_abundance = 0, core_max_abundance = 0, core_all_aver ... [TRUNCATED]
     seed=NULL,dist='Bray-Curtis',representative='mean',rescale_core=FALSE, use_microViz = 'yes')

Rd file 'FourHnull.Rd':
  \usage lines wider than 90 characters:
                   sample_no, null_model=1,replace_hosts=FALSE, reads=NULL, rarefy_each_step=TRUE,seed=NULL, use_microViz='yes')

Rd file 'FourHpreanalysis.Rd':
  \usage lines wider than 90 characters:
     FourHpreanalysis(x, class_grouping, core_fraction, boot_no, sample_no, core_average_abundance = 0, core_max_abundance = 0, core_all_ave ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* 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 ... ERROR
Running examples in 'HybridMicrobiomes-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FourHbootstrapA
> ### Title: Bootstraps of the abundance-based 4H Index
> ### Aliases: FourHbootstrapA
> 
> ### ** Examples
> 
> #Test with enterotype dataset
> library(phyloseq)
> data(enterotype)
> #Covert the OTU table to reads, rather than fractional abundances
> otu_table(enterotype)<-round(10000*otu_table(enterotype))
> 
> #Randomly assign host classes (these should be known in a real hybrid microbiome dataset)
> #The two parent species are assigned '1' and '3' respectively, the hybrid is assigned '2'
> hybrid_status<-sample(1:3,280, replace=TRUE)
> 
> FourHbootstrapA(enterotype,hybrid_status,0.5,5,10)
Error in loadNamespace(x) : there is no package called 'microViz'
Calls: FourHbootstrapA ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking PDF version of manual ... [13s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 5 NOTEs