* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/schtools.Rcheck’
* using R Under development (unstable) (2025-09-09 r88801)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
    GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘schtools/DESCRIPTION’ ... OK
* this is package ‘schtools’ version ‘0.4.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘hrbrthemes’
* 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 ‘schtools’ can be installed ... [7s/24s] OK
* checking package directory ... 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 ... 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 ... [9s/28s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘schtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: calc_relabun
> ### Title: Calculate OTU relative abundances from a shared file
> ### Aliases: calc_relabun
> 
> ### ** Examples
> 
> shared_dat <- readr::read_tsv(system.file("extdata", "test.shared",
+   package = "schtools"
+ ))
Error in loadNamespace(x) : there is no package called ‘readr’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [5s/15s]
 [5s/17s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(schtools)
  > 
  > test_check("schtools")
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 42 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plot.R:1:1'): (code run outside of `test_that()`) ──────────────
  <packageNotFoundError/error/condition>
  Error in `library(ggplot2)`: there is no package called 'ggplot2'
  Backtrace:
      ▆
   1. └─base::library(ggplot2) at test-plot.R:1:1
  ── Error ('test-read_tax.R:5:1'): (code run outside of `test_that()`) ──────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'readr'
  Backtrace:
      ▆
   1. └─base::loadNamespace(x) at test-read_tax.R:5:1
   2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   3.     └─base (local) withOneRestart(expr, restarts[[1L]])
   4.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 42 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [7s/20s] 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: 2 ERRORs
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/schtools.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:32.13, 60.57 + 9.41