CRAN Package Check Results for Package beadplexr

Last updated on 2019-11-26 00:51:45 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.0 9.79 273.06 282.85 ERROR
r-devel-linux-x86_64-debian-gcc 0.2.0 8.72 201.65 210.37 ERROR
r-devel-linux-x86_64-fedora-clang 0.2.0 405.15 OK
r-devel-linux-x86_64-fedora-gcc 0.2.0 406.58 OK
r-devel-windows-ix86+x86_64 0.2.0 34.00 439.00 473.00 OK
r-devel-windows-ix86+x86_64-gcc8 0.2.0 31.00 351.00 382.00 OK
r-patched-linux-x86_64 0.2.0 9.55 337.20 346.75 OK
r-patched-solaris-x86 0.2.0 642.80 OK
r-release-linux-x86_64 0.2.0 9.17 348.04 357.21 OK
r-release-windows-ix86+x86_64 0.2.0 29.00 323.00 352.00 OK
r-release-osx-x86_64 0.2.0 OK
r-oldrel-windows-ix86+x86_64 0.2.0 12.00 435.00 447.00 OK
r-oldrel-osx-x86_64 0.2.0 OK

Check Details

Version: 0.2.0
Check: examples
Result: ERROR
    Running examples in 'beadplexr-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: read_fcs
    > ### Title: Read a fcs file.
    > ### Aliases: read_fcs
    >
    > ### ** Examples
    >
    > library(beadplexr)
    >
    > .file_name <- system.file("extdata", "K2-C07-A7.fcs",
    + package = "beadplexr")
    >
    > # Load the fcs file, with no filter
    > .data <- read_fcs(.file_name = .file_name, .filter = NULL)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    beadplexr
     --- call from context ---
    .f(.x[[i]], ...)
     --- call from argument ---
    if ((class(.x) == "matrix") & is.numeric(.x)) {
     TRUE %in% (.p %in% colnames(.x))
    } else {
     FALSE
    }
     --- R stacktrace ---
    where 1: .f(.x[[i]], ...)
    where 2: purrr::map_lgl(., .get_potential_comp_matrices, .p = ff_parameters)
    where 3: function_list[[k]](value)
    where 4: withVisible(function_list[[k]](value))
    where 5: freduce(value, `_function_list`)
    where 6: `_fseq`(`_lhs`)
    where 7: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 8: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 9: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
    where 10: ff_keywords %>% purrr::map_lgl(.get_potential_comp_matrices,
     .p = ff_parameters)
    where 11: apply_compensation(., .compensation = .compensation)
    where 12: function_list[[i]](value)
    where 13: freduce(value, `_function_list`)
    where 14: `_fseq`(`_lhs`)
    where 15: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 16: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 17: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
    where 18: flowCore::read.FCS(filename = .file_name, transformation = FALSE,
     ...) %>% transform_bead_channels(.bead_channels = .bead_channels) %>%
     apply_compensation(.compensation = .compensation) %>% remove_boundary_events(.channels = c(.fsc_ssc)) %>%
     subset_channels(.filter = .filter) %>% as_data_frame_flow_frame(.channels = c(.fsc_ssc,
     .bead_channels))
    where 19: read_fcs(.file_name = .file_name, .filter = NULL)
    
     --- value of length: 2 type: logical ---
    [1] TRUE FALSE
     --- function from context ---
    function (.x, .p)
    {
     if ((class(.x) == "matrix") & is.numeric(.x)) {
     TRUE %in% (.p %in% colnames(.x))
     }
     else {
     FALSE
     }
    }
    <bytecode: 0x14e61848>
    <environment: 0x14e5d500>
     --- function search by body ---
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.2.0
Check: tests
Result: ERROR
     Running 'testthat.R' [139s/155s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(beadplexr)
     >
     > test_check("beadplexr")
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     beadplexr
     --- call from context ---
     .f(.x[[i]], ...)
     --- call from argument ---
     if ((class(.x) == "matrix") & is.numeric(.x)) {
     TRUE %in% (.p %in% colnames(.x))
     } else {
     FALSE
     }
     --- R stacktrace ---
     where 1: .f(.x[[i]], ...)
     where 2: purrr::map_lgl(., .get_potential_comp_matrices, .p = ff_parameters)
     where 3: function_list[[k]](value)
     where 4: withVisible(function_list[[k]](value))
     where 5: freduce(value, `_function_list`)
     where 6: `_fseq`(`_lhs`)
     where 7: eval(quote(`_fseq`(`_lhs`)), env, env)
     where 8: eval(quote(`_fseq`(`_lhs`)), env, env)
     where 9: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
     where 10: ff_keywords %>% purrr::map_lgl(.get_potential_comp_matrices,
     .p = ff_parameters)
     where 11: apply_compensation(.flow_frame = .flow_frame, .compensation = "guess")
     where 12: eval_bare(expr, quo_get_env(quo))
     where 13: quasi_label(enquo(object), label, arg = "object")
     where 14 at testthat/test_read_fcs.R#55: expect_is(apply_compensation(.flow_frame = .flow_frame, .compensation = "guess"),
     "flowFrame")
     where 15: eval(code, test_env)
     where 16: eval(code, test_env)
     where 17: 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 18: doTryCatch(return(expr), name, parentenv, handler)
     where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 21: doTryCatch(return(expr), name, parentenv, handler)
     where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 23: tryCatchList(expr, classes, parentenv, handlers)
     where 24: 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 25: test_code(desc, code, env = parent.frame())
     where 26 at testthat/test_read_fcs.R#53: test_that("Compensation can be applied", {
     expect_is(apply_compensation(.flow_frame = .flow_frame, .compensation = NULL),
     "flowFrame")
     expect_is(apply_compensation(.flow_frame = .flow_frame, .compensation = "guess"),
     "flowFrame")
     expect_is(apply_compensation(.flow_frame = .flow_frame, .compensation = "SPILL"),
     "flowFrame")
     expect_is(apply_compensation(.flow_frame = .flow_frame, .compensation = "spillover"),
     "flowFrame")
     expect_is(apply_compensation(.flow_frame = .flow_frame, .compensation = comp_matrix),
     "flowFrame")
     expect_warning(apply_compensation(.flow_frame = .flow_frame,
     .compensation = c("guess", "xxx")))
     expect_warning(apply_compensation(.flow_frame = .flow_frame,
     .compensation = "xxx"))
     expect_warning(apply_compensation(.flow_frame = odd_ff, .compensation = "guess"))
     expect_warning(apply_compensation(.flow_frame = odd_ff, .compensation = "spill"))
     expect_error(apply_compensation(.flow_frame = odd_ff, .compensation = list(list("guess",
     "XXX"))))
     expect_error(apply_compensation(.flow_frame = odd_ff, .compensation = data.frame("guess",
     "XXX")))
     })
     where 27: eval(code, test_env)
     where 28: eval(code, test_env)
     where 29: 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 30: doTryCatch(return(expr), name, parentenv, handler)
     where 31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 32: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 33: doTryCatch(return(expr), name, parentenv, handler)
     where 34: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 35: tryCatchList(expr, classes, parentenv, handlers)
     where 36: 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 37: test_code(NULL, exprs, env)
     where 38: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     where 39: force(code)
     where 40: doWithOneRestart(return(expr), restart)
     where 41: withOneRestart(expr, restarts[[1L]])
     where 42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 43: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
     {
     reporter$start_file(basename(path))
     lister$start_file(basename(path))
     source_file(path, new.env(parent = env), chdir = TRUE,
     wrap = wrap)
     reporter$.end_context()
     reporter$end_file()
     })
     where 44: FUN(X[[i]], ...)
     where 45: lapply(paths, test_file, env = env, reporter = current_reporter,
     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     where 46: force(code)
     where 47: doWithOneRestart(return(expr), restart)
     where 48: withOneRestart(expr, restarts[[1L]])
     where 49: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 50: with_reporter(reporter = current_reporter, results <- lapply(paths,
     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
     load_helpers = FALSE, wrap = wrap))
     where 51: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 52: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
     wrap = wrap)
     where 53: test_package_dir(package = package, test_path = test_path, filter = filter,
     reporter = reporter, ..., stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 54: test_check("beadplexr")
    
     --- value of length: 2 type: logical ---
     [1] TRUE FALSE
     --- function from context ---
     function (.x, .p)
     {
     if ((class(.x) == "matrix") & is.numeric(.x)) {
     TRUE %in% (.p %in% colnames(.x))
     }
     else {
     FALSE
     }
     }
     <bytecode: 0x73c34d8>
     <environment: 0xdc23968>
     --- function search by body ---
     ----------- END OF FAILURE REPORT --------------
     Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.2.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'cba_macsplex_example.Rmd' using rmarkdown
    --- finished re-building 'cba_macsplex_example.Rmd'
    
    --- re-building 'legendplex-analysis.Rmd' using rmarkdown
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    beadplexr
     --- call from context ---
    .f(.x[[i]], ...)
     --- call from argument ---
    if ((class(.x) == "matrix") & is.numeric(.x)) {
     TRUE %in% (.p %in% colnames(.x))
    } else {
     FALSE
    }
     --- R stacktrace ---
    where 1: .f(.x[[i]], ...)
    where 2: purrr::map_lgl(., .get_potential_comp_matrices, .p = ff_parameters)
    where 3: function_list[[k]](value)
    where 4: withVisible(function_list[[k]](value))
    where 5: freduce(value, `_function_list`)
    where 6: `_fseq`(`_lhs`)
    where 7: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 8: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 9: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
    where 10: ff_keywords %>% purrr::map_lgl(.get_potential_comp_matrices,
     .p = ff_parameters)
    where 11: apply_compensation(., .compensation = .compensation)
    where 12: function_list[[i]](value)
    where 13: freduce(value, `_function_list`)
    where 14: `_fseq`(`_lhs`)
    where 15: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 16: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 17: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
    where 18: flowCore::read.FCS(filename = .file_name, transformation = FALSE,
     ...) %>% transform_bead_channels(.bead_channels = .bead_channels) %>%
     apply_compensation(.compensation = .compensation) %>% remove_boundary_events(.channels = c(.fsc_ssc)) %>%
     subset_channels(.filter = .filter) %>% as_data_frame_flow_frame(.channels = c(.fsc_ssc,
     .bead_channels))
    where 19: read_fcs(.file_name = .file_name)
    where 20: eval(expr, envir, enclos)
    where 21: eval(expr, envir, enclos)
    where 22: withVisible(eval(expr, envir, enclos))
    where 23: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 24: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 25: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 26: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 27: evaluate::evaluate(...)
    where 28: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
     options$include) 0L else 2L, output_handler = knit_handlers(options$render,
     options))
    where 29: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
     stop_on_error = if (options$error && options$include) 0L else 2L,
     output_handler = knit_handlers(options$render, options)))
    where 30: block_exec(params)
    where 31: call_block(x)
    where 32: process_group.block(group)
    where 33: process_group(group)
    where 34: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 35: process_file(text, output)
    where 36: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet,
     encoding = encoding)
    where 37: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     ...)
    where 38: vweave_rmarkdown(...)
    where 39: engine$weave(file, quiet = quiet, encoding = enc)
    where 40: doTryCatch(return(expr), name, parentenv, handler)
    where 41: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 42: tryCatchList(expr, classes, parentenv, handlers)
    where 43: tryCatch({
     engine$weave(file, quiet = quiet, encoding = enc)
     setwd(startdir)
     output <- find_vignette_product(name, by = "weave", engine = engine)
     if (!have.makefile && vignette_is_tex(output)) {
     texi2pdf(file = output, clean = FALSE, quiet = quiet)
     output <- find_vignette_product(name, by = "texi2pdf",
     engine = engine)
     }
    }, error = function(e) {
     OK <<- FALSE
     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
     file, conditionMessage(e)))
    })
    where 44: tools:::.buildOneVignette("legendplex-analysis.Rmd", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/beadplexr.Rcheck/vign_test/beadplexr",
     TRUE, FALSE, "legendplex-analysis", "UTF-8", "/tmp/Rtmplm4y3y/file55c5233ceea2.rds")
    
     --- value of length: 2 type: logical ---
    [1] TRUE FALSE
     --- function from context ---
    function (.x, .p)
    {
     if ((class(.x) == "matrix") & is.numeric(.x)) {
     TRUE %in% (.p %in% colnames(.x))
     }
     else {
     FALSE
     }
    }
    <bytecode: 0x6293b20>
    <environment: 0x6295d50>
     --- function search by body ---
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
    SUMMARY: processing the following file failed:
     'legendplex-analysis.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.2.0
Check: examples
Result: ERROR
    Running examples in ‘beadplexr-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: read_fcs
    > ### Title: Read a fcs file.
    > ### Aliases: read_fcs
    >
    > ### ** Examples
    >
    > library(beadplexr)
    >
    > .file_name <- system.file("extdata", "K2-C07-A7.fcs",
    + package = "beadplexr")
    >
    > # Load the fcs file, with no filter
    > .data <- read_fcs(.file_name = .file_name, .filter = NULL)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    beadplexr
     --- call from context ---
    .f(.x[[i]], ...)
     --- call from argument ---
    if ((class(.x) == "matrix") & is.numeric(.x)) {
     TRUE %in% (.p %in% colnames(.x))
    } else {
     FALSE
    }
     --- R stacktrace ---
    where 1: .f(.x[[i]], ...)
    where 2: purrr::map_lgl(., .get_potential_comp_matrices, .p = ff_parameters)
    where 3: function_list[[k]](value)
    where 4: withVisible(function_list[[k]](value))
    where 5: freduce(value, `_function_list`)
    where 6: `_fseq`(`_lhs`)
    where 7: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 8: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 9: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
    where 10: ff_keywords %>% purrr::map_lgl(.get_potential_comp_matrices,
     .p = ff_parameters)
    where 11: apply_compensation(., .compensation = .compensation)
    where 12: function_list[[i]](value)
    where 13: freduce(value, `_function_list`)
    where 14: `_fseq`(`_lhs`)
    where 15: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 16: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 17: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
    where 18: flowCore::read.FCS(filename = .file_name, transformation = FALSE,
     ...) %>% transform_bead_channels(.bead_channels = .bead_channels) %>%
     apply_compensation(.compensation = .compensation) %>% remove_boundary_events(.channels = c(.fsc_ssc)) %>%
     subset_channels(.filter = .filter) %>% as_data_frame_flow_frame(.channels = c(.fsc_ssc,
     .bead_channels))
    where 19: read_fcs(.file_name = .file_name, .filter = NULL)
    
     --- value of length: 2 type: logical ---
    [1] TRUE FALSE
     --- function from context ---
    function (.x, .p)
    {
     if ((class(.x) == "matrix") & is.numeric(.x)) {
     TRUE %in% (.p %in% colnames(.x))
     }
     else {
     FALSE
     }
    }
    <bytecode: 0x55897d9ce2b0>
    <environment: 0x55897d9b6940>
     --- function search by body ---
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [101s/143s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(beadplexr)
     >
     > test_check("beadplexr")
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     beadplexr
     --- call from context ---
     .f(.x[[i]], ...)
     --- call from argument ---
     if ((class(.x) == "matrix") & is.numeric(.x)) {
     TRUE %in% (.p %in% colnames(.x))
     } else {
     FALSE
     }
     --- R stacktrace ---
     where 1: .f(.x[[i]], ...)
     where 2: purrr::map_lgl(., .get_potential_comp_matrices, .p = ff_parameters)
     where 3: function_list[[k]](value)
     where 4: withVisible(function_list[[k]](value))
     where 5: freduce(value, `_function_list`)
     where 6: `_fseq`(`_lhs`)
     where 7: eval(quote(`_fseq`(`_lhs`)), env, env)
     where 8: eval(quote(`_fseq`(`_lhs`)), env, env)
     where 9: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
     where 10: ff_keywords %>% purrr::map_lgl(.get_potential_comp_matrices,
     .p = ff_parameters)
     where 11: apply_compensation(.flow_frame = .flow_frame, .compensation = "guess")
     where 12: eval_bare(expr, quo_get_env(quo))
     where 13: quasi_label(enquo(object), label, arg = "object")
     where 14 at testthat/test_read_fcs.R#55: expect_is(apply_compensation(.flow_frame = .flow_frame, .compensation = "guess"),
     "flowFrame")
     where 15: eval(code, test_env)
     where 16: eval(code, test_env)
     where 17: 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 18: doTryCatch(return(expr), name, parentenv, handler)
     where 19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 20: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 21: doTryCatch(return(expr), name, parentenv, handler)
     where 22: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 23: tryCatchList(expr, classes, parentenv, handlers)
     where 24: 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 25: test_code(desc, code, env = parent.frame())
     where 26 at testthat/test_read_fcs.R#53: test_that("Compensation can be applied", {
     expect_is(apply_compensation(.flow_frame = .flow_frame, .compensation = NULL),
     "flowFrame")
     expect_is(apply_compensation(.flow_frame = .flow_frame, .compensation = "guess"),
     "flowFrame")
     expect_is(apply_compensation(.flow_frame = .flow_frame, .compensation = "SPILL"),
     "flowFrame")
     expect_is(apply_compensation(.flow_frame = .flow_frame, .compensation = "spillover"),
     "flowFrame")
     expect_is(apply_compensation(.flow_frame = .flow_frame, .compensation = comp_matrix),
     "flowFrame")
     expect_warning(apply_compensation(.flow_frame = .flow_frame,
     .compensation = c("guess", "xxx")))
     expect_warning(apply_compensation(.flow_frame = .flow_frame,
     .compensation = "xxx"))
     expect_warning(apply_compensation(.flow_frame = odd_ff, .compensation = "guess"))
     expect_warning(apply_compensation(.flow_frame = odd_ff, .compensation = "spill"))
     expect_error(apply_compensation(.flow_frame = odd_ff, .compensation = list(list("guess",
     "XXX"))))
     expect_error(apply_compensation(.flow_frame = odd_ff, .compensation = data.frame("guess",
     "XXX")))
     })
     where 27: eval(code, test_env)
     where 28: eval(code, test_env)
     where 29: 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 30: doTryCatch(return(expr), name, parentenv, handler)
     where 31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 32: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 33: doTryCatch(return(expr), name, parentenv, handler)
     where 34: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 35: tryCatchList(expr, classes, parentenv, handlers)
     where 36: 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 37: test_code(NULL, exprs, env)
     where 38: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     where 39: force(code)
     where 40: doWithOneRestart(return(expr), restart)
     where 41: withOneRestart(expr, restarts[[1L]])
     where 42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 43: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
     {
     reporter$start_file(basename(path))
     lister$start_file(basename(path))
     source_file(path, new.env(parent = env), chdir = TRUE,
     wrap = wrap)
     reporter$.end_context()
     reporter$end_file()
     })
     where 44: FUN(X[[i]], ...)
     where 45: lapply(paths, test_file, env = env, reporter = current_reporter,
     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     where 46: force(code)
     where 47: doWithOneRestart(return(expr), restart)
     where 48: withOneRestart(expr, restarts[[1L]])
     where 49: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 50: with_reporter(reporter = current_reporter, results <- lapply(paths,
     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
     load_helpers = FALSE, wrap = wrap))
     where 51: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 52: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
     wrap = wrap)
     where 53: test_package_dir(package = package, test_path = test_path, filter = filter,
     reporter = reporter, ..., stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 54: test_check("beadplexr")
    
     --- value of length: 2 type: logical ---
     [1] TRUE FALSE
     --- function from context ---
     function (.x, .p)
     {
     if ((class(.x) == "matrix") & is.numeric(.x)) {
     TRUE %in% (.p %in% colnames(.x))
     }
     else {
     FALSE
     }
     }
     <bytecode: 0x562034d2ea50>
     <environment: 0x56203d356780>
     --- function search by body ---
     ----------- END OF FAILURE REPORT --------------
     Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘cba_macsplex_example.Rmd’ using rmarkdown
    --- finished re-building ‘cba_macsplex_example.Rmd’
    
    --- re-building ‘legendplex-analysis.Rmd’ using rmarkdown
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    beadplexr
     --- call from context ---
    .f(.x[[i]], ...)
     --- call from argument ---
    if ((class(.x) == "matrix") & is.numeric(.x)) {
     TRUE %in% (.p %in% colnames(.x))
    } else {
     FALSE
    }
     --- R stacktrace ---
    where 1: .f(.x[[i]], ...)
    where 2: purrr::map_lgl(., .get_potential_comp_matrices, .p = ff_parameters)
    where 3: function_list[[k]](value)
    where 4: withVisible(function_list[[k]](value))
    where 5: freduce(value, `_function_list`)
    where 6: `_fseq`(`_lhs`)
    where 7: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 8: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 9: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
    where 10: ff_keywords %>% purrr::map_lgl(.get_potential_comp_matrices,
     .p = ff_parameters)
    where 11: apply_compensation(., .compensation = .compensation)
    where 12: function_list[[i]](value)
    where 13: freduce(value, `_function_list`)
    where 14: `_fseq`(`_lhs`)
    where 15: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 16: eval(quote(`_fseq`(`_lhs`)), env, env)
    where 17: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
    where 18: flowCore::read.FCS(filename = .file_name, transformation = FALSE,
     ...) %>% transform_bead_channels(.bead_channels = .bead_channels) %>%
     apply_compensation(.compensation = .compensation) %>% remove_boundary_events(.channels = c(.fsc_ssc)) %>%
     subset_channels(.filter = .filter) %>% as_data_frame_flow_frame(.channels = c(.fsc_ssc,
     .bead_channels))
    where 19: read_fcs(.file_name = .file_name)
    where 20: eval(expr, envir, enclos)
    where 21: eval(expr, envir, enclos)
    where 22: withVisible(eval(expr, envir, enclos))
    where 23: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 24: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 25: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 26: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 27: evaluate::evaluate(...)
    where 28: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
     options$include) 0L else 2L, output_handler = knit_handlers(options$render,
     options))
    where 29: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
     stop_on_error = if (options$error && options$include) 0L else 2L,
     output_handler = knit_handlers(options$render, options)))
    where 30: block_exec(params)
    where 31: call_block(x)
    where 32: process_group.block(group)
    where 33: process_group(group)
    where 34: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 35: process_file(text, output)
    where 36: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet,
     encoding = encoding)
    where 37: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     ...)
    where 38: vweave_rmarkdown(...)
    where 39: engine$weave(file, quiet = quiet, encoding = enc)
    where 40: doTryCatch(return(expr), name, parentenv, handler)
    where 41: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 42: tryCatchList(expr, classes, parentenv, handlers)
    where 43: tryCatch({
     engine$weave(file, quiet = quiet, encoding = enc)
     setwd(startdir)
     output <- find_vignette_product(name, by = "weave", engine = engine)
     if (!have.makefile && vignette_is_tex(output)) {
     texi2pdf(file = output, clean = FALSE, quiet = quiet)
     output <- find_vignette_product(name, by = "texi2pdf",
     engine = engine)
     }
    }, error = function(e) {
     OK <<- FALSE
     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
     file, conditionMessage(e)))
    })
    where 44: tools:::.buildOneVignette("legendplex-analysis.Rmd", "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/beadplexr.Rcheck/vign_test/beadplexr",
     TRUE, FALSE, "legendplex-analysis", "UTF-8", "/home/hornik/tmp/scratch/RtmpVj2dgl/filecb8e3a0186.rds")
    
     --- value of length: 2 type: logical ---
    [1] TRUE FALSE
     --- function from context ---
    function (.x, .p)
    {
     if ((class(.x) == "matrix") & is.numeric(.x)) {
     TRUE %in% (.p %in% colnames(.x))
     }
     else {
     FALSE
     }
    }
    <bytecode: 0x558ba6930ce8>
    <environment: 0x558ba6933110>
     --- function search by body ---
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
    SUMMARY: processing the following file failed:
     ‘legendplex-analysis.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc