CRAN Package Check Results for Package crmn

Last updated on 2020-01-20 01:50:18 CET.

Check Details

Version: 0.0.20
Check: R code for possible problems
Result: NOTE
    makeX_eset: no visible global function definition for 'model.matrix'
    normFit: no visible binding for global variable 'lm'
    normFit: no visible binding for global variable 'sd'
    normFit: no visible global function definition for 'lm'
    normPred: no visible binding for global variable 'predict'
    normPred: no visible global function definition for 'predict'
    normPred: no visible binding for global variable 'median'
    plot.nFit: no visible global function definition for 'par'
    plot.nFit: no visible global function definition for 'barplot'
    plot.nFit: no visible global function definition for 'legend'
    show_nfit: no visible global function definition for 'anova'
    show_nfit: no visible global function definition for 'residuals'
    show_nfit: no visible global function definition for 'fitted'
    standardsFit: no visible binding for global variable 'lm'
    standardsFit: no visible global function definition for 'resid'
    standardsFit: no visible global function definition for
     'compareVersion'
    standardsPred: no visible global function definition for 'predict'
    makeX,ExpressionSet-character: no visible global function definition
     for 'model.matrix'
    plot,nFit: no visible global function definition for 'par'
    plot,nFit: no visible global function definition for 'barplot'
    plot,nFit: no visible global function definition for 'legend'
    show,nFit: no visible global function definition for 'anova'
    show,nFit: no visible global function definition for 'residuals'
    show,nFit: no visible global function definition for 'fitted'
    Undefined global functions or variables:
     anova barplot compareVersion fitted legend lm median model.matrix par
     predict resid residuals sd
    Consider adding
     importFrom("graphics", "barplot", "legend", "par")
     importFrom("stats", "anova", "fitted", "lm", "median", "model.matrix",
     "predict", "resid", "residuals", "sd")
     importFrom("utils", "compareVersion")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.0.20
Check: examples
Result: ERROR
    Running examples in 'crmn-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: normalize
    > ### Title: Normalize a metabolomics dataset
    > ### Aliases: normalize
    >
    > ### ** Examples
    >
    > data(mix)
    > normalize(mix, "crmn", factor="type", ncomp=3)
    ExpressionSet (storageMode: lockedEnvironment)
    assayData: 35 features, 42 samples
     element names: exprs
    protocolData: none
    phenoData
     sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
     varLabels: type experiment runorder
     varMetadata: labelDescription
    featureData
     featureNames: 15 18 ... 249 (35 total)
     fvarLabels: mark tag ... preferred (7 total)
     fvarMetadata: labelDescription
    experimentData: use 'experimentData(object)'
    Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
    > #other methods
    > normalize(mix, "one")
    ExpressionSet (storageMode: lockedEnvironment)
    assayData: 35 features, 42 samples
     element names: exprs
    protocolData: none
    phenoData
     sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
     varLabels: type experiment runorder
     varMetadata: labelDescription
    featureData
     featureNames: 15 18 ... 249 (35 total)
     fvarLabels: mark tag ... preferred (7 total)
     fvarMetadata: labelDescription
    experimentData: use 'experimentData(object)'
    Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
    > normalize(mix, "avg")
    ExpressionSet (storageMode: lockedEnvironment)
    assayData: 35 features, 42 samples
     element names: exprs
    protocolData: none
    phenoData
     sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
     varLabels: type experiment runorder
     varMetadata: labelDescription
    featureData
     featureNames: 15 18 ... 249 (35 total)
     fvarLabels: mark tag ... preferred (7 total)
     fvarMetadata: labelDescription
    experimentData: use 'experimentData(object)'
    Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
    > normalize(mix, "nomis")
    ExpressionSet (storageMode: lockedEnvironment)
    assayData: 35 features, 42 samples
     element names: exprs
    protocolData: none
    phenoData
     sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
     varLabels: type experiment runorder
     varMetadata: labelDescription
    featureData
     featureNames: 15 18 ... 249 (35 total)
     fvarLabels: mark tag ... preferred (7 total)
     fvarMetadata: labelDescription
    experimentData: use 'experimentData(object)'
    Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
    > normalize(mix, "t1")
    ExpressionSet (storageMode: lockedEnvironment)
    assayData: 35 features, 42 samples
     element names: exprs
    protocolData: none
    phenoData
     sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
     varLabels: type experiment runorder
     varMetadata: labelDescription
    featureData
     featureNames: 15 18 ... 249 (35 total)
     fvarLabels: mark tag ... preferred (7 total)
     fvarMetadata: labelDescription
    experimentData: use 'experimentData(object)'
    Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
    > normalize(mix, "ri")
    ExpressionSet (storageMode: lockedEnvironment)
    assayData: 35 features, 42 samples
     element names: exprs
    protocolData: none
    phenoData
     sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
     varLabels: type experiment runorder
     varMetadata: labelDescription
    featureData
     featureNames: 15 18 ... 249 (35 total)
     fvarLabels: mark tag ... preferred (7 total)
     fvarMetadata: labelDescription
    experimentData: use 'experimentData(object)'
    Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
    > normalize(mix, "median")
    ExpressionSet (storageMode: lockedEnvironment)
    assayData: 35 features, 42 samples
     element names: exprs
    protocolData: none
    phenoData
     sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
     varLabels: type experiment runorder
     varMetadata: labelDescription
    featureData
     featureNames: 15 18 ... 249 (35 total)
     fvarLabels: mark tag ... preferred (7 total)
     fvarMetadata: labelDescription
    experimentData: use 'experimentData(object)'
    Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
    > normalize(mix, "totL2")
    ExpressionSet (storageMode: lockedEnvironment)
    assayData: 35 features, 42 samples
     element names: exprs
    protocolData: none
    phenoData
     sampleNames: STDs_1_2_1 STDs_1_2_2 ... STDs3_3_11 (42 total)
     varLabels: type experiment runorder
     varMetadata: labelDescription
    featureData
     featureNames: 15 18 ... 249 (35 total)
     fvarLabels: mark tag ... preferred (7 total)
     fvarMetadata: labelDescription
    experimentData: use 'experimentData(object)'
    Annotation: readGCMS(expfile = "../../data/081228_tomato02_dilution_nv_MetMat_ABS/081228_tomato02_dilution_MetMat_abs.txt", pdatafile = "../../data/pheno2.csv", convid = function(x) gsub("_Di", "", x), standards = TRUE, tables = "preferred")
    > ## can also do normalization with matrices
    > Y <- exprs(mix)
    > G <- with(pData(mix), model.matrix(~-1+type))
    > isIS <- with(fData(mix), tag == "IS")
    > normalize(Y, "crmn", factor=G, ncomp=3, standards=isIS)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    crmn
     --- call from context ---
    normalize(Y, "crmn", factor = G, ncomp = 3, standards = isIS)
     --- call from argument ---
    if (class(object) == "ExpressionSet") pData(object) <- dropunusedlevels(pData(object))
     --- R stacktrace ---
    where 1: normalize(Y, "crmn", factor = G, ncomp = 3, standards = isIS)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (object, method, segments = NULL, ...)
    {
     if (class(object) == "ExpressionSet")
     pData(object) <- dropunusedlevels(pData(object))
     if (is.null(segments)) {
     fit <- normFit(object, method = method, ...)
     object <- normPred(fit, object, ...)
     }
     else {
     anaobj <- analytes(object, ...)
     exprMat <- mexprs(anaobj)
     for (i in segments) {
     fit <- normFit(object[, -i], method = method, ...)
     exprMat[, i] <- mexprs(normPred(fit, object[, i],
     ...))
     }
     mexprs(anaobj) <- exprMat
     object <- anaobj
     }
     object
    }
    <bytecode: 0x69a3d78>
    <environment: namespace:crmn>
     --- function search by body ---
    Function normalize in namespace crmn has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(object) == "ExpressionSet") pData(object) <- dropunusedlevels(pData(object)) :
     the condition has length > 1
    Calls: normalize
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.0.20
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'crmn.Rnw' using Sweave
    Loading required package: pcaMethods
    Loading required package: Biobase
    Loading required package: BiocGenerics
    Loading required package: parallel
    
    Attaching package: 'BiocGenerics'
    
    The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
    The following objects are masked from 'package:stats':
    
     IQR, mad, sd, var, xtabs
    
    The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, basename, cbind, colnames, dirname, do.call,
     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max, which.min
    
    Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
    
    Attaching package: 'pcaMethods'
    
    The following object is masked from 'package:stats':
    
     loadings
    
    
    Attaching package: 'crmn'
    
    The following object is masked from 'package:BiocGenerics':
    
     normalize
    
    
     Information on package 'crmn'
    
    Description:
    
    Package: crmn
    Version: 0.0.20
    Date: 2012-06-19
    Author: Henning Redestig
    Maintainer: Henning Redestig <henning.red@gmail.com>
    Title: CCMN and other noRMalizatioN methods for
     metabolomics data
    Depends: R (>= 2.10), pcaMethods (>= 1.56.0), Biobase,
     methods
    Description: Implements the Cross-contribution Compensating
     Multiple standard Normalization (CCMN) method and
     other normalization algorithms.
    License: GPL (>= 3)
    Collate: 'classes.R' 'crmn-package.R' 'norm.R' 'misc.R'
     'generic.R'
    Packaged: 2014-11-20 00:07:23 UTC; henning
    Repository: CRAN
    Date/Publication: 2014-11-20 08:08:19
    NeedsCompilation: no
    Built: R 4.0.0; ; 2020-01-16 14:29:56 UTC; unix
    
    Index:
    
    analytes Accessor for the analytes
    analytes_eset Accessor for the analytes
    analytes_other Accessor for the analytes
    crmn CRMN
    dropunusedlevels Drop unused levels
    makeX-methods Make X
    method-methods Accessor for the method
    mexprs-methods Matrix safe accessor of expression slot
    mexprs-rep-methods Accessor
    mix Dilution mixture dataset.
    model-methods Accessor for the model
    nFit Normalization model
    normFit Fit a normalization model
    normPred Predict for normalization
    normalize Normalize a metabolomics dataset
    pcaMuffle Muffle the pca function
    plot.nFit Plot a statistics for CRMN normalization model
    sFit-method Accessor for the standards model
    show Show method for nFit
    show_nfit Show nfit
    standards Accessor for the Internal Standards
    standardsFit Standards model
    standardsPred Predict effect for new data (or get fitted
     data)
    standards_eset Accessor for the Internal Standards
    standards_other Accessor for the Internal Standards
    weightnorm Normalize by sample weight
    
    Further information is available in the following vignettes in
    directory
    '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/crmn/doc':
    
    crmn: Introduction/Tutorial (source, pdf)
    
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    crmn
     --- call from context ---
    normalize(Y, "crmn", factors = G, standards = isIS, ncomp = 2)
     --- call from argument ---
    if (class(object) == "ExpressionSet") pData(object) <- dropunusedlevels(pData(object))
     --- R stacktrace ---
    where 1: normalize(Y, "crmn", factors = G, standards = isIS, ncomp = 2)
    where 2: eval(expr, .GlobalEnv)
    where 3: eval(expr, .GlobalEnv)
    where 4: withVisible(eval(expr, .GlobalEnv))
    where 5: doTryCatch(return(expr), name, parentenv, handler)
    where 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 7: tryCatchList(expr, classes, parentenv, handlers)
    where 8: tryCatch(expr, error = function(e) {
     call <- conditionCall(e)
     if (!is.null(call)) {
     if (identical(call[[1L]], quote(doTryCatch)))
     call <- sys.call(-4L)
     dcall <- deparse(call)[1L]
     prefix <- paste("Error in", dcall, ": ")
     LONG <- 75L
     sm <- strsplit(conditionMessage(e), "\n")[[1L]]
     w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
     if (is.na(w))
     w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
     type = "b")
     if (w > LONG)
     prefix <- paste0(prefix, "\n ")
     }
     else prefix <- "Error : "
     msg <- paste0(prefix, conditionMessage(e), "\n")
     .Internal(seterrmessage(msg[1L]))
     if (!silent && isTRUE(getOption("show.error.messages"))) {
     cat(msg, file = outFile)
     .Internal(printDeferredWarnings())
     }
     invisible(structure(msg, class = "try-error", condition = e))
    })
    where 9: try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE)
    where 10: evalFunc(ce, options)
    where 11: tryCatchList(expr, classes, parentenv, handlers)
    where 12: tryCatch(evalFunc(ce, options), finally = {
     cat("\n")
     sink()
    })
    where 13: driver$runcode(drobj, chunk, chunkopts)
    where 14: utils::Sweave(...)
    where 15: engine$weave(file, quiet = quiet, encoding = enc)
    where 16: doTryCatch(return(expr), name, parentenv, handler)
    where 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 18: tryCatchList(expr, classes, parentenv, handlers)
    where 19: 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 20: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/crmn.Rcheck/vign_test/crmn",
     ser_elibs = "/tmp/RtmpLwcJCP/file77f036012907.rds")
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (object, method, segments = NULL, ...)
    {
     if (class(object) == "ExpressionSet")
     pData(object) <- dropunusedlevels(pData(object))
     if (is.null(segments)) {
     fit <- normFit(object, method = method, ...)
     object <- normPred(fit, object, ...)
     }
     else {
     anaobj <- analytes(object, ...)
     exprMat <- mexprs(anaobj)
     for (i in segments) {
     fit <- normFit(object[, -i], method = method, ...)
     exprMat[, i] <- mexprs(normPred(fit, object[, i],
     ...))
     }
     mexprs(anaobj) <- exprMat
     object <- anaobj
     }
     object
    }
    <bytecode: 0x68278f0>
    <environment: namespace:crmn>
     --- function search by body ---
    Function normalize in namespace crmn has this body.
     ----------- END OF FAILURE REPORT --------------
    
    Error: processing vignette 'crmn.Rnw' failed with diagnostics:
     chunk 16 (label = alternative)
    Error in if (class(object) == "ExpressionSet") pData(object) <- dropunusedlevels(pData(object)) :
     the condition has length > 1
    
    --- failed re-building 'crmn.Rnw'
    
    SUMMARY: processing the following file failed:
     'crmn.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang