* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/RevGadgets.Rcheck’
* using R Under development (unstable) (2022-04-03 r82074)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘RevGadgets/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RevGadgets’ version ‘1.0.0’
* 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 ‘RevGadgets’ can be installed ... [17s/29s] OK
* checking package 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 ... [32s/44s] 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 examples ... [9s/14s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [16s/22s]
 [16s/23s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RevGadgets)
  > 
  > test_check("RevGadgets")
  
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   ----------- FAILURE REPORT -------------- 
   --- failure: length > 1 in coercion to logical ---
   --- srcref --- 
  : 
   --- package (from environment) --- 
  ggtree
   --- call from context --- 
  ggpie(df, y = ~value, fill = ~type, color, alpha)
   --- call from argument --- 
  missingArg(color) || is.null(color) || is.na(color)
   --- R stacktrace ---
  where 1: ggpie(df, y = ~value, fill = ~type, color, alpha)
  where 2: FUN(X[[i]], ...)
  where 3: lapply(ldf, function(df) ggpie(df, y = ~value, fill = ~type, 
      color, alpha))
  where 4: ggtree::nodepie(dat_state_start, cols = 1:(ncol(dat_state_start) - 
      1), color = colors, alpha = state_transparency)
  where 5 at test_plotAncStatesPie.R#41: plotAncStatesPie(t = dec_example, pie_colors = colors, tip_labels_size = 2, 
      cladogenetic = TRUE, tip_labels_offset = 0.01, timeline = F, 
      node_pie_size = 0.5, tip_pie_size = 0.3)
  where 6: eval(code, test_env)
  where 7: eval(code, test_env)
  where 8: 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 9: doTryCatch(return(expr), name, parentenv, handler)
  where 10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 11: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  where 12: doTryCatch(return(expr), name, parentenv, handler)
  where 13: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), 
      names[nh], parentenv, handlers[[nh]])
  where 14: tryCatchList(expr, classes, parentenv, handlers)
  where 15: 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 16: test_code(desc, code, env = parent.frame(), reporter = reporter)
  where 17 at test_plotAncStatesPie.R#3: test_that("plots pies of ancestral states", {
      tree_file <- system.file("extdata", "dec/small_dec.tre", 
          package = "RevGadgets")
      plot_file <- system.file("extdata", "graphs/plotAncStatesPie_df.rds", 
          package = "RevGadgets")
      labs <- c(`1` = "K", `2` = "O", `3` = "M", `4` = "H", `5` = "KO", 
          `6` = "KM", `7` = "OM", `8` = "KH", `9` = "OH", `10` = "MH", 
          `11` = "KOM", `12` = "KOH", `13` = "KMH", `14` = "OMH", 
          `15` = "KOMH")
      dec_example <- processAncStates(tree_file, state_labels = labs)
      colors <- colorRampPalette(colFun(12))(length(dec_example@state_labels))
      names(colors) <- dec_example@state_labels
      plot_new <- plotAncStatesPie(t = dec_example, pie_colors = colors, 
          tip_labels_size = 2, cladogenetic = TRUE, tip_labels_offset = 0.01, 
          timeline = F, node_pie_size = 0.5, tip_pie_size = 0.3) + 
          ggplot2::scale_x_continuous(limits = c(-0.5, 1)) + ggplot2::theme(legend.position = c(0.1, 
          0.75))
      plot_orig <- readRDS(plot_file)
      tmp <- tempdir()
      pdf(paste0(tmp, "/Rplots.pdf"))
      expect_error(print(plot_new), NA)
      dev.off()
      expect_equal(plot_new$data, plot_orig)
  })
  where 18: eval(code, test_env)
  where 19: eval(code, test_env)
  where 20: withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error)
  where 21: doTryCatch(return(expr), name, parentenv, handler)
  where 22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 23: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  where 24: doTryCatch(return(expr), name, parentenv, handler)
  where 25: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), 
      names[nh], parentenv, handlers[[nh]])
  where 26: tryCatchList(expr, classes, parentenv, handlers)
  where 27: tryCatch(withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error), error = handle_fatal, 
      skip = function(e) {
      })
  where 28: test_code(NULL, exprs, env)
  where 29: source_file(path, child_env(env), wrap = wrap)
  where 30: FUN(X[[i]], ...)
  where 31: lapply(test_paths, test_one_file, env = env, wrap = wrap)
  where 32: doTryCatch(return(expr), name, parentenv, handler)
  where 33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 34: tryCatchList(expr, classes, parentenv, handlers)
  where 35: tryCatch(code, testthat_abort_reporter = function(cnd) {
      cat(conditionMessage(cnd), "\n")
      NULL
  })
  where 36: with_reporter(reporters$multi, lapply(test_paths, test_one_file, 
      env = env, wrap = wrap))
  where 37: 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 38: 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 39: test_dir("testthat", package = package, reporter = reporter, 
      ..., load_package = "installed")
  where 40: test_check("RevGadgets")
  
   --- value of length: 5 type: logical ---
     KM     M    MH    OM other 
  FALSE FALSE FALSE FALSE FALSE 
   --- function from context --- 
  function (data, y, fill, color, alpha = 1) 
  {
      p <- ggplot(data, aes_(x = 1, y = y, fill = fill)) + geom_bar(stat = "identity", 
          alpha = alpha) + coord_polar(theta = "y") + theme_inset()
      if (missingArg(color) || is.null(color) || is.na(color)) {
      }
      else {
          p <- p + scale_fill_manual(values = color)
      }
      return(p)
  }
  <bytecode: 0x103c1290>
  <environment: namespace:ggtree>
   --- function search by body ---
  Function ggpie in namespace ggtree has this body.
   ----------- END OF FAILURE REPORT -------------- 
  Fatal error: length > 1 in coercion to logical
* 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: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/RevGadgets.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:36.12, 132.50 + 11.64