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; ; 2020-02-09 14:30:25 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/RtmpO4ZKxK/file1b456c947fee.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: 0x7785800>
<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