Last updated on 2019-12-21 10:48:02 CET.
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
---|---|---|---|---|---|---|
r-devel-linux-x86_64-debian-clang | 0.1.0 | 37.30 | 325.94 | 363.24 | ERROR | |
r-devel-linux-x86_64-debian-gcc | 0.1.0 | 29.54 | 257.73 | 287.27 | ERROR | |
r-devel-linux-x86_64-fedora-clang | 0.1.0 | 549.90 | OK | |||
r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 428.49 | OK | |||
r-devel-windows-ix86+x86_64 | 0.1.0 | 93.00 | 880.00 | 973.00 | OK | |
r-devel-windows-ix86+x86_64-gcc8 | 0.1.0 | 122.00 | 868.00 | 990.00 | NOTE | |
r-patched-linux-x86_64 | 0.1.0 | OK | ||||
r-patched-solaris-x86 | 0.1.0 | 601.70 | OK | |||
r-release-linux-x86_64 | 0.1.0 | 30.10 | 317.03 | 347.13 | OK | |
r-release-windows-ix86+x86_64 | 0.1.0 | 68.00 | 871.00 | 939.00 | OK | |
r-release-osx-x86_64 | 0.1.0 | OK | ||||
r-oldrel-windows-ix86+x86_64 | 0.1.0 | 55.00 | 788.00 | 843.00 | OK | |
r-oldrel-osx-x86_64 | 0.1.0 | OK |
Version: 0.1.0
Check: tests
Result: ERROR
Running 'testthat.R' [32s/40s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(themetagenomics)
Loading required package: Rcpp
>
> test_check("themetagenomics")
-- 1. Failure: prepare_data works with no formula (@test-prepare.R#11) --------
list("matrix", NULL, NULL, NULL, NULL, NULL, NULL) not identical to c(class(x[[1]]), unname(x[2:7])).
Length mismatch: comparison on first 7 components
Component 2: target is NULL, current is character
-- 2. Failure: prepare_data works with no formula (@test-prepare.R#17) --------
list("matrix", NULL, NULL, NULL, NULL, NULL, NULL) not identical to c(class(x[[1]]), unname(x[2:7])).
Length mismatch: comparison on first 7 components
Component 2: target is NULL, current is character
-- 3. Failure: prepare_data works with binary factor (@test-prepare.R#37) -----
list(...) not identical to unname(lapply(x, class)).
Component 1: Lengths (1, 2) differ (string compare on first 1)
Component 2: Lengths (1, 2) differ (string compare on first 1)
-- 4. Failure: prepare_data works with continuous covariate (@test-prepare.R#55)
list(...) not identical to unname(lapply(x, class)).
Component 1: Lengths (1, 2) differ (string compare on first 1)
Component 2: Lengths (1, 2) differ (string compare on first 1)
-- 5. Failure: prepare_data works with spline covariate (@test-prepare.R#73) --
list(...) not identical to unname(lapply(x, class)).
Component 1: Lengths (1, 2) differ (string compare on first 1)
Component 2: Lengths (1, 2) differ (string compare on first 1)
-- 6. Failure: prepare_data works with multiclass factor (@test-prepare.R#105)
list(...) not identical to unname(lapply(x, class)).
Component 1: Lengths (1, 2) differ (string compare on first 1)
Component 2: Lengths (1, 2) differ (string compare on first 1)
-- 7. Failure: prepare_data works with multiclass factor and continuous (@test-p
list(...) not identical to unname(lapply(x, class)).
Component 1: Lengths (1, 2) differ (string compare on first 1)
Component 2: Lengths (1, 2) differ (string compare on first 1)
-- 8. Failure: prepare_data works with multiclass factor and spline (@test-prepa
list(...) not identical to unname(lapply(x, class)).
Component 1: Lengths (1, 2) differ (string compare on first 1)
Component 2: Lengths (1, 2) differ (string compare on first 1)
== testthat results ===========================================================
[ OK: 48 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 8 ]
1. Failure: prepare_data works with no formula (@test-prepare.R#11)
2. Failure: prepare_data works with no formula (@test-prepare.R#17)
3. Failure: prepare_data works with binary factor (@test-prepare.R#37)
4. Failure: prepare_data works with continuous covariate (@test-prepare.R#55)
5. Failure: prepare_data works with spline covariate (@test-prepare.R#73)
6. Failure: prepare_data works with multiclass factor (@test-prepare.R#105)
7. Failure: prepare_data works with multiclass factor and continuous (@test-prepare.R#123)
8. Failure: prepare_data works with multiclass factor and spline (@test-prepare.R#151)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'functional_prediction.Rmd' using rmarkdown
--- finished re-building 'functional_prediction.Rmd'
--- re-building 'thematic_structure.Rmd' using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
themetagenomics
--- call from context ---
create_multiclasses_table(estimated_effects$modelframe, estimated_effects$modelframe_full,
spline_idx)
--- call from argument ---
if (class(multiclasses) == "list") {
out <- cbind(full = names(sapply(modelframe_full, class)),
do.call("rbind", multiclasses))
rownames(out) <- NULL
} else {
out <- cbind(colnames(modelframe_full), t(multiclasses))
colnames(out) <- c("full", "baseclass", "multiclass", "lev",
"ref")
rownames(out) <- NULL
}
--- R stacktrace ---
where 1: create_multiclasses_table(estimated_effects$modelframe, estimated_effects$modelframe_full,
spline_idx)
where 2: est_topics_backend(estimated_effects, fit$theta, nsims = nsims,
ui_level = ui_level, npoints = npoints, verbose = verbose)
where 3: est.topics(TOPICS)
where 4: est(TOPICS)
where 5: system.time(TOPIC_EFFECTS <- est(TOPICS))
where 6: eval(expr, envir, enclos)
where 7: eval(expr, envir, enclos)
where 8: withVisible(eval(expr, envir, enclos))
where 9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 10: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 12: evaluate_call(expr, parsed$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 13: evaluate::evaluate(...)
where 14: 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$render,
options))
where 15: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$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 16: block_exec(params)
where 17: call_block(x)
where 18: process_group.block(group)
where 19: process_group(group)
where 20: 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$get("infile"),
") ")
})
where 21: process_file(text, output)
where 22: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 23: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
...)
where 24: vweave_rmarkdown(...)
where 25: engine$weave(file, quiet = quiet, encoding = enc)
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: 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 30: tools:::.buildOneVignette("thematic_structure.Rmd", "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/themetagenomics.Rcheck/vign_test/themetagenomics",
TRUE, FALSE, "thematic_structure", "UTF-8", "/tmp/RtmpSQvR8x/file3c213b959ace.rds")
--- value of length: 2 type: logical ---
[1] FALSE FALSE
--- function from context ---
function (modelframe, modelframe_full, splines = NULL)
{
classes <- sapply(modelframe, class)
classes[classes == "integer"] <- "numeric"
multiclasses <- classes
multiclasses[which(sapply(modelframe, function(x) length(levels(x))) >
2)] <- "multiclass"
multiclasses[splines] <- "spline"
multiclasses <- sapply(seq_along(multiclasses), function(i) {
if (classes[i] == "factor") {
j <- length(levels(modelframe[, i])) - 1
baseclass <- rep(classes[i], j)
multiclass <- rep(multiclasses[i], j)
lev <- levels(modelframe[, i])[-1]
ref <- levels(modelframe[, i])[1]
}
else {
j <- 1
baseclass <- rep(classes[i], j)
multiclass <- rep(multiclasses[i], j)
lev <- 2
ref <- 1
}
cbind(baseclass, multiclass, lev, ref)
})
if (class(multiclasses) == "list") {
out <- cbind(full = names(sapply(modelframe_full, class)),
do.call("rbind", multiclasses))
rownames(out) <- NULL
}
else {
out <- cbind(colnames(modelframe_full), t(multiclasses))
colnames(out) <- c("full", "baseclass", "multiclass",
"lev", "ref")
rownames(out) <- NULL
}
out <- data.frame(out, stringsAsFactors = FALSE)
return(out)
}
<bytecode: 0xbd48fc0>
<environment: namespace:themetagenomics>
--- function search by body ---
Function create_multiclasses_table in namespace themetagenomics has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 103-104 (thematic_structure.Rmd)
Error: processing vignette 'thematic_structure.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'thematic_structure.Rmd'
SUMMARY: processing the following file failed:
'thematic_structure.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [25s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(themetagenomics)
Loading required package: Rcpp
>
> test_check("themetagenomics")
── 1. Failure: prepare_data works with no formula (@test-prepare.R#11) ────────
list("matrix", NULL, NULL, NULL, NULL, NULL, NULL) not identical to c(class(x[[1]]), unname(x[2:7])).
Length mismatch: comparison on first 7 components
Component 2: target is NULL, current is character
── 2. Failure: prepare_data works with no formula (@test-prepare.R#17) ────────
list("matrix", NULL, NULL, NULL, NULL, NULL, NULL) not identical to c(class(x[[1]]), unname(x[2:7])).
Length mismatch: comparison on first 7 components
Component 2: target is NULL, current is character
── 3. Failure: prepare_data works with binary factor (@test-prepare.R#37) ─────
list(...) not identical to unname(lapply(x, class)).
Component 1: Lengths (1, 2) differ (string compare on first 1)
Component 2: Lengths (1, 2) differ (string compare on first 1)
── 4. Failure: prepare_data works with continuous covariate (@test-prepare.R#55)
list(...) not identical to unname(lapply(x, class)).
Component 1: Lengths (1, 2) differ (string compare on first 1)
Component 2: Lengths (1, 2) differ (string compare on first 1)
── 5. Failure: prepare_data works with spline covariate (@test-prepare.R#73) ──
list(...) not identical to unname(lapply(x, class)).
Component 1: Lengths (1, 2) differ (string compare on first 1)
Component 2: Lengths (1, 2) differ (string compare on first 1)
── 6. Failure: prepare_data works with multiclass factor (@test-prepare.R#105)
list(...) not identical to unname(lapply(x, class)).
Component 1: Lengths (1, 2) differ (string compare on first 1)
Component 2: Lengths (1, 2) differ (string compare on first 1)
── 7. Failure: prepare_data works with multiclass factor and continuous (@test-p
list(...) not identical to unname(lapply(x, class)).
Component 1: Lengths (1, 2) differ (string compare on first 1)
Component 2: Lengths (1, 2) differ (string compare on first 1)
── 8. Failure: prepare_data works with multiclass factor and spline (@test-prepa
list(...) not identical to unname(lapply(x, class)).
Component 1: Lengths (1, 2) differ (string compare on first 1)
Component 2: Lengths (1, 2) differ (string compare on first 1)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 48 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 8 ]
1. Failure: prepare_data works with no formula (@test-prepare.R#11)
2. Failure: prepare_data works with no formula (@test-prepare.R#17)
3. Failure: prepare_data works with binary factor (@test-prepare.R#37)
4. Failure: prepare_data works with continuous covariate (@test-prepare.R#55)
5. Failure: prepare_data works with spline covariate (@test-prepare.R#73)
6. Failure: prepare_data works with multiclass factor (@test-prepare.R#105)
7. Failure: prepare_data works with multiclass factor and continuous (@test-prepare.R#123)
8. Failure: prepare_data works with multiclass factor and spline (@test-prepare.R#151)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: installed package size
Result: NOTE
installed size is 5.0Mb
sub-directories of 1Mb or more:
libs 2.2Mb
references 1.1Mb
Flavor: r-devel-windows-ix86+x86_64-gcc8