* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/bioset.Rcheck’
* using R Under development (unstable) (2022-04-26 r82260)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘bioset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bioset’ version ‘0.2.3’
* package encoding: UTF-8
* 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 ‘bioset’ can be installed ... [4s/10s] 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 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 ... [6s/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 LazyData ... NOTE
  'LazyData' is specified without a 'data' directory
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/12s] ERROR
Running examples in ‘bioset-Ex.R’ failed
The error most likely occurred in:

> ### Name: calc_factor_conc
> ### Title: Get a factor to convert concentrations.
> ### Aliases: calc_factor_conc
> 
> ### ** Examples
> 
> library("dplyr")

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> 
> # generate test data
> data <- tibble(
+   sample = c("A", "B", "C"),
+   conc = c(4.5, 2.3, 5.1),       # concentration in g  / l
+ )
> 
> fctr_ng_ml <- calc_factor_conc(from = "g/l", to = "ng/ml")
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
bioset
 --- call from context --- 
is_recognised_unit(parts)
 --- call from argument --- 
is.character(x) && nchar(x) > 0
 --- R stacktrace ---
where 1: is_recognised_unit(parts)
where 2: FALSE %in% is_recognised_unit(parts)
where 3: canonicalise_units(from)
where 4: calc_factor_conc(from = "g/l", to = "ng/ml")

 --- value of length: 2 type: logical ---
[1] TRUE TRUE
 --- function from context --- 
function (x) 
{
    if (is.character(x) && nchar(x) > 0) {
        return(x %in% recognised_units)
    }
    return(FALSE)
}
<bytecode: 0x67b8500>
<environment: namespace:bioset>
 --- function search by body ---
Function is_recognised_unit in namespace bioset has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bioset)
  > 
  > test_check("bioset")
   ----------- FAILURE REPORT -------------- 
   --- failure: length > 1 in coercion to logical ---
   --- srcref --- 
  : 
   --- package (from environment) --- 
  bioset
   --- call from context --- 
  is_recognised_unit(parts)
   --- call from argument --- 
  is.character(x) && nchar(x) > 0
   --- R stacktrace ---
  where 1: is_recognised_unit(parts)
  where 2: FALSE %in% is_recognised_unit(parts)
  where 3: bioset:::canonicalise_units(" µ l / \tf g\t")
  where 4: eval_bare(expr, quo_get_env(quo))
  where 5: quasi_label(enquo(object), label, arg = "object")
  where 6 at test_calc.R#6: expect_equal(bioset:::canonicalise_units(" µ l / \tf g\t"), 
      "µl/fg")
  where 7: eval(code, test_env)
  where 8: eval(code, test_env)
  where 9: withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error)
  where 10: doTryCatch(return(expr), name, parentenv, handler)
  where 11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 12: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  where 13: doTryCatch(return(expr), name, parentenv, handler)
  where 14: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), 
      names[nh], parentenv, handlers[[nh]])
  where 15: tryCatchList(expr, classes, parentenv, handlers)
  where 16: tryCatch(withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error), error = handle_fatal, 
      skip = function(e) {
      })
  where 17: test_code(desc, code, env = parent.frame(), reporter = reporter)
  where 18 at test_calc.R#4: test_that("canonicalise_units works as expected", {
      expect_equal(bioset:::canonicalise_units("   µ   l   "), 
          "µl")
      expect_equal(bioset:::canonicalise_units(" µ l / \tf g\t"), 
          "µl/fg")
      expect_error(bioset:::canonicalise_units("%"))
      expect_error(bioset:::canonicalise_units(""))
      expect_error(bioset:::canonicalise_units(" \t "))
      expect_error(bioset:::canonicalise_units(" \t / \t"))
      expect_error(bioset:::canonicalise_units(" %\t / \t"))
      expect_error(bioset:::canonicalise_units(" %"))
      expect_warning(bioset:::canonicalise_units("% w / v"))
      expect_warning(bioset:::canonicalise_units("%w/v"))
      expect_equal(bioset:::canonicalise_units("v/v"), "l/l")
      expect_equal(bioset:::canonicalise_units("w/w"), "g/g")
      expect_equal(bioset:::canonicalise_units("%v/v"), "cl/l")
      expect_equal(bioset:::canonicalise_units("%w/w"), "cg/g")
      expect_equal(bioset:::canonicalise_units("µM"), "µmol/l")
      expect_equal(bioset:::canonicalise_units("M"), "mol/l")
  })
  where 19: eval(code, test_env)
  where 20: eval(code, test_env)
  where 21: withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error)
  where 22: doTryCatch(return(expr), name, parentenv, handler)
  where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 24: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  where 25: doTryCatch(return(expr), name, parentenv, handler)
  where 26: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), 
      names[nh], parentenv, handlers[[nh]])
  where 27: tryCatchList(expr, classes, parentenv, handlers)
  where 28: tryCatch(withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error), error = handle_fatal, 
      skip = function(e) {
      })
  where 29: test_code(NULL, exprs, env)
  where 30: source_file(path, child_env(env), wrap = wrap)
  where 31: FUN(X[[i]], ...)
  where 32: lapply(test_paths, test_one_file, env = env, wrap = wrap)
  where 33: doTryCatch(return(expr), name, parentenv, handler)
  where 34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 35: tryCatchList(expr, classes, parentenv, handlers)
  where 36: tryCatch(code, testthat_abort_reporter = function(cnd) {
      cat(conditionMessage(cnd), "\n")
      NULL
  })
  where 37: with_reporter(reporters$multi, lapply(test_paths, test_one_file, 
      env = env, wrap = wrap))
  where 38: test_files(test_dir = test_dir, test_package = test_package, 
      test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, 
      env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 
      wrap = wrap, load_package = load_package)
  where 39: test_files(test_dir = path, test_paths = test_paths, test_package = package, 
      reporter = reporter, load_helpers = load_helpers, env = env, 
      stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 
      wrap = wrap, load_package = load_package, parallel = parallel)
  where 40: test_dir("testthat", package = package, reporter = reporter, 
      ..., load_package = "installed")
  where 41: test_check("bioset")
  
   --- value of length: 2 type: logical ---
  [1] TRUE TRUE
   --- function from context --- 
  function (x) 
  {
      if (is.character(x) && nchar(x) > 0) {
          return(x %in% recognised_units)
      }
      return(FALSE)
  }
  <bytecode: 0x1dd4150>
  <environment: namespace:bioset>
   --- function search by body ---
  Function is_recognised_unit in namespace bioset has this body.
   ----------- END OF FAILURE REPORT -------------- 
  Fatal error: length > 1 in coercion to logical
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [6s/17s] OK
* checking PDF 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, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/bioset.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 2:16.46, 43.97 + 7.13