CRAN Package Check Results for Package themetagenomics

Last updated on 2019-12-21 10:48:02 CET.

Check Details

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