* using log directory ‘/srv/hornik/tmp/CRAN_pretest/clustur.Rcheck’
* using R Under development (unstable) (2024-11-11 r87319)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.1 (1)
    Debian flang-new version 19.1.1 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘clustur/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clustur’ version ‘0.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/8s] NOTE
Maintainer: ‘Patrick Schloss <pschloss@umich.edu>’

New submission

Possibly misspelled words in DESCRIPTION:
  OptiClust (14:329)
  SL (14:445)
  Westcott (14:436)
  al (14:90)
  clustur (14:130)
  et (14:87)
  mothur (14:68, 14:195)
* 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 whether package ‘clustur’ can be installed ... [130s/130s] OK
* used C++ compiler: ‘Debian clang version 19.1.3 (1)’
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [5s/5s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] ERROR
Running examples in ‘clustur-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_dist
> ### Title: Read distance matrices
> ### Aliases: read_dist
> 
> ### ** Examples
> 
> 
>  i_values <- as.integer(1:100)
>  j_values <- as.integer(sample(1:100, 100, TRUE))
>  x_values <- as.numeric(runif(100, 0, 1))
>  s_matrix <- create_sparse_matrix(i_values, j_values, x_values)
> 
>  sparse_count <- data.frame(
+                  Representative_Sequence = 1:100,
+                  total = rep(1, times = 100))
> 
>  column_path <- example_path("amazon_column.dist")
>  phylip_path <- example_path("amazon_phylip.dist")
>  count_table <- read_count(example_path("amazon.full.count_table"))
> 
>  data_column <- read_dist(column_path, count_table, 0.03)
>  data_phylip <- read_dist(phylip_path, count_table, 0.03)
Error: These names were not found in the count table:
98
Please ensure all names in the distance file are in the count table
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [2s/2s] ERROR
  Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(clustur)
  > 
  > test_check("clustur")
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 249 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-test-opticluster.R:52:3'): Opticluster works with phylip files ──
  <Rcpp::exception/C++Error/error/condition>
  Error: These names were not found in the count table:
  98
  Please ensure all names in the distance file are in the count table
  Backtrace:
      ▆
   1. └─clustur::read_dist(...) at test-test-opticluster.R:52:3
   2.   └─clustur:::ProcessDistanceFiles(...)
  ── Error ('test-test-opticluster.R:72:3'): cluster works via phylip file ───────
  <Rcpp::exception/C++Error/error/condition>
  Error: These names were not found in the count table:
  98
  Please ensure all names in the distance file are in the count table
  Backtrace:
      ▆
   1. └─clustur::read_dist(...) at test-test-opticluster.R:72:3
   2.   └─clustur:::ProcessDistanceFiles(...)
  ── Error ('test-test-opticluster.R:157:3'): Read dist can read column, phylip files, and sparse matrices ──
  <Rcpp::exception/C++Error/error/condition>
  Error: These names were not found in the count table:
  98
  Please ensure all names in the distance file are in the count table
  Backtrace:
      ▆
   1. └─clustur::read_dist(...) at test-test-opticluster.R:157:3
   2.   └─clustur:::ProcessDistanceFiles(...)
  ── Failure ('test-test-opticluster.R:200:3'): We can determine if a file is phylip or not ──
  `is_phylip` is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 249 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [1s/1s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘clustur.Rmd’ using rmarkdown

Quitting from lines 82-83 [unnamed-chunk-4] (clustur.Rmd)
Error: processing vignette 'clustur.Rmd' failed with diagnostics:
These names were not found in the count table:
98
Please ensure all names in the distance file are in the count table
--- failed re-building ‘clustur.Rmd’

SUMMARY: processing the following file failed:
  ‘clustur.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [2s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 3 ERRORs, 1 NOTE