CRAN Package Check Results for Package NormalizeMets

Last updated on 2020-01-27 00:48:09 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.25 13.49 140.41 153.90 ERROR
r-devel-linux-x86_64-debian-gcc 0.25 11.31 138.13 149.44 OK
r-devel-linux-x86_64-fedora-clang 0.25 232.08 NOTE
r-devel-linux-x86_64-fedora-gcc 0.25 226.83 NOTE
r-devel-windows-ix86+x86_64 0.25 41.00 277.00 318.00 NOTE
r-devel-windows-ix86+x86_64-gcc8 0.25 41.00 284.00 325.00 NOTE
r-patched-linux-x86_64 0.25 10.45 164.74 175.19 OK
r-patched-solaris-x86 0.25 190.50 WARN
r-release-linux-x86_64 0.25 11.63 162.41 174.04 OK
r-release-windows-ix86+x86_64 0.25 24.00 183.00 207.00 NOTE
r-release-osx-x86_64 0.25 WARN
r-oldrel-windows-ix86+x86_64 0.25 17.00 202.00 219.00 NOTE
r-oldrel-osx-x86_64 0.25 WARN

Check Details

Version: 0.25
Check: examples
Result: ERROR
    Running examples in 'NormalizeMets-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: ComparePvalHist
    > ### Title: p-value Histogram
    > ### Aliases: ComparePvalHist
    >
    > ### ** Examples
    >
    > data("alldata_eg")
    > featuredata_eg<-alldata_eg$featuredata
    > dataview(featuredata_eg)
    
     - The data consists of 150 rows by 128 columns
    
     m_1 m_2 m_3 m_4 m_5 m_6 m_7
    s_1 10485.867 33220.562 1112.9795 1408.6396 455.7529 1100.4023 122.36316
    s_2 8960.469 29995.516 926.2891 529.0449 873.6094 2201.2461 173.08020
    s_3 10160.445 28559.641 1230.3330 1306.3203 1027.5078 2066.5918 269.79980
    s_4 8794.477 27593.750 901.7622 1800.0830 675.0396 1675.8496 287.99927
    s_5 8956.922 28161.766 979.1724 818.0366 904.0254 1245.9912 167.41333
    s_6 9092.258 31685.312 634.6899 478.3811 980.4233 1259.5635 97.56250
    s_7 2271.045 7692.176 143.1688 109.8399 730.6172 1387.7920 149.09668
    s_8 7850.402 26462.797 822.5991 1341.2158 583.5830 2164.1270 227.76965
    s_9 10969.062 21605.141 408.0005 1499.4795 452.2375 916.5283 234.49756
    s_10 1743.933 7647.645 218.4199 127.4294 408.2913 999.5718 74.82697
     m_8 ...
    s_1 3855.805 ...
    s_2 5090.637 ...
    s_3 4483.906 ...
    s_4 4949.262 ...
    s_5 4302.934 ...
    s_6 4406.344 ...
    s_7 1543.406 ...
    s_8 5030.688 ...
    s_9 4657.254 ...
    s_10 1510.012 ...
    > sampledata_eg<-alldata_eg$sampledata
    > dataview(sampledata_eg)
    
     - The data consists of 150 rows by 4 columns
    
     batch gender Age bmi
    s_1 Batch 2 code_1 58.66 22.22
    s_2 Batch 2 code_0 76.70 23.74
    s_3 Batch 2 code_0 56.15 28.19
    s_4 Batch 2 code_0 77.22 26.18
    s_5 Batch 2 code_0 74.29 26.37
    s_6 Batch 2 code_1 66.82 26.39
    s_7 Batch 1 code_0 65.00 29.00
    s_8 Batch 2 code_1 66.51 26.13
    s_9 Batch 2 code_0 70.23 27.26
    s_10 Batch 1 code_1 55.00 25.00
    > metabolitedata_eg<-alldata_eg$metabolitedata
    > dataview(metabolitedata_eg)
    
     - The data consists of 128 rows by 4 columns
    
     names IS neg_controls pos_controls_gender
    1 m_1 0 1 0
    2 m_2 0 1 0
    3 m_3 0 1 0
    4 m_4 0 0 0
    5 m_5 0 0 0
    6 m_6 0 0 0
    7 m_7 0 0 0
    8 m_8 0 1 0
    9 m_9 0 1 0
    10 m_10 0 1 0
    >
    > logdata <- LogTransform(featuredata_eg)
    > dataview(logdata$featuredata)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    NormalizeMets
     --- call from context ---
    dataview(logdata$featuredata)
     --- call from argument ---
    if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe")
     --- R stacktrace ---
    where 1: dataview(logdata$featuredata)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (data)
    {
     if (class(data) %in% c("list"))
     stop("Input data must be a vector, a matrix, or a dataframe")
     data <- as.data.frame(data)
     hdata <- data
     dsize <- dim(hdata)
     if (dsize[1] > 10) {
     hdata <- hdata[1:10, ]
     }
     if (dsize[2] > 8) {
     hdata <- hdata[, 1:9]
     hdata[, 9] <- rep("...", nrow(hdata))
     colnames(hdata)[9] <- "..."
     }
     write(paste("\n - The data consists of ", dsize[1], " rows by ",
     dsize[2], " columns \n", sep = ""), "")
     return(hdata)
    }
    <bytecode: 0x4985920>
    <environment: namespace:NormalizeMets>
     --- function search by body ---
    Function dataview in namespace NormalizeMets has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe") :
     the condition has length > 1
    Calls: dataview
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.25
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'NormalizeMets_vignette.Rmd' using rmarkdown
    Warning in if (class(object) == "ExpressionSet") pData(object) <- dropunusedlevels(pData(object)) :
     the condition has length > 1 and only the first element will be used
    Warning in if (class(object) == "ExpressionSet") pData(object) <- dropunusedlevels(pData(object)) :
     the condition has length > 1 and only the first element will be used
    Warning: Zero sample variances detected, have been offset away from zero
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    NormalizeMets
     --- call from context ---
    dataview(uv_ruvrandclust$featuredata)
     --- call from argument ---
    if (class(data) %in% c("list")) stop("Input data must be a vector, a matrix, or a dataframe")
     --- R stacktrace ---
    where 1: dataview(uv_ruvrandclust$featuredata)
    where 2: eval(expr, envir, enclos)
    where 3: eval(expr, envir, enclos)
    where 4: withVisible(eval(expr, envir, enclos))
    where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 9: evaluate::evaluate(...)
    where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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 11: 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$render, options)))
    where 12: block_exec(params)
    where 13: call_block(x)
    where 14: process_group.block(group)
    where 15: process_group(group)
    where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 17: process_file(text, output)
    where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     output_dir = getwd(), ...)
    where 20: vweave_rmarkdown(...)
    where 21: engine$weave(file, quiet = quiet, encoding = enc)
    where 22: doTryCatch(return(expr), name, parentenv, handler)
    where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 24: tryCatchList(expr, classes, parentenv, handlers)
    where 25: tryCatch({
     engine$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)
     }
     outputs <- c(outputs, output)
    }, error = function(e) {
     thisOK <<- FALSE
     fails <<- c(fails, file)
     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
     file, conditionMessage(e)))
    })
    where 26: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/NormalizeMets.Rcheck/vign_test/NormalizeMets",
     ser_elibs = "/tmp/RtmpNn2ri7/file5cd25c3c903f.rds")
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (data)
    {
     if (class(data) %in% c("list"))
     stop("Input data must be a vector, a matrix, or a dataframe")
     data <- as.data.frame(data)
     hdata <- data
     dsize <- dim(hdata)
     if (dsize[1] > 10) {
     hdata <- hdata[1:10, ]
     }
     if (dsize[2] > 8) {
     hdata <- hdata[, 1:9]
     hdata[, 9] <- rep("...", nrow(hdata))
     colnames(hdata)[9] <- "..."
     }
     write(paste("\n - The data consists of ", dsize[1], " rows by ",
     dsize[2], " columns \n", sep = ""), "")
     return(hdata)
    }
    <bytecode: 0x78d3248>
    <environment: namespace:NormalizeMets>
     --- function search by body ---
    Function dataview in namespace NormalizeMets has this body.
     ----------- END OF FAILURE REPORT --------------
    Quitting from lines 458-472 (NormalizeMets_vignette.Rmd)
    Error: processing vignette 'NormalizeMets_vignette.Rmd' failed with diagnostics:
    the condition has length > 1
    --- failed re-building 'NormalizeMets_vignette.Rmd'
    
    SUMMARY: processing the following file failed:
     'NormalizeMets_vignette.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.25
Check: installed package size
Result: NOTE
     installed size is 9.3Mb
     sub-directories of 1Mb or more:
     doc 8.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.25
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘knitr’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.25
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘NormalizeMets_vignette.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 192-194 (NormalizeMets_vignette.Rmd)
    Error: processing vignette 'NormalizeMets_vignette.Rmd' failed with diagnostics:
    Saving a widget with selfcontained = TRUE requires pandoc. For details see:
    https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
    --- failed re-building ‘NormalizeMets_vignette.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘NormalizeMets_vignette.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavors: r-patched-solaris-x86, r-release-osx-x86_64

Version: 0.25
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Quitting from lines 192-194 (NormalizeMets_vignette.Rmd)
    Error: processing vignette 'NormalizeMets_vignette.Rmd' failed with diagnostics:
    Saving a widget with selfcontained = TRUE requires pandoc. For details see:
    https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
    Execution halted
Flavor: r-oldrel-osx-x86_64