Multiple platform build/check report for BioC 3.6 - BUILD report for DASC on malbec1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data DASC
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* checking for file ‘DASC/DESCRIPTION’ ... OK
* preparing ‘DASC’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Warning: 'html_document2' is deprecated.
Use 'html_document' instead.
See help("Deprecated")
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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect,
    is.unsorted, lapply, lengths, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    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")'.

Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:base':

    isNamespaceLoaded

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [NO: synchronicity] | Cores 19/20
  To enable shared memory capabilities, try: install.extras('
NMF
')
Loading required package: cvxclustr
Loading required package: Matrix
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:NMF':

    algorithm, compare

The following objects are masked from 'package:BiocGenerics':

    normalize, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:Matrix':

    expand

The following object is masked from 'package:NMF':

    nrun

The following object is masked from 'package:pkgmaker':

    new2

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:NMF':

    seed

The following object is masked from 'package:base':

    apply


factor levels were dropped which had no samples
Timing stopped at: 1.56 0.824 1.932
ERROR
Timing stopped at: 1.84 0.996 2.371
ERROR
Quitting from lines 164-167 (DASC_html.Rmd) 
Error: processing vignette 'DASC_html.Rmd' failed with diagnostics:
All the runs produced an error:
	-#1 [r=2] -> NMF::nmf - 10/10 fit(s) threw an error.
# Error(s) thrown:
  - run #1: unused arguments (model = list(model = "NMFstd", rank = 2, target = 0), method = function (model, target) 
{
    N <- ncol(target)
    ans <- kmeans(t(target), nbasis(model))
    G0 <- matrix(0, nrow = N, ncol = nbasis(model))
    for (i in 1:N) {
        G0[i, ans$cluster[i]] <- 1
    }
    G0 <- G0 + 0.2
    coef(model) <- t(G0)
    basis(model) <- target %*% G0 %*% solve(t(G0) %*% G0)
    return(model)
})
	-#2 [r=3] -> NMF::nmf - 10/10 fit(s) threw an error.
# Error(s) thrown:
  - run #1: unused arguments (model = list(model = "NMFstd", rank = 3, target = 0), method = function (model, target) 
{
    N <- ncol(target)
    ans <- kmeans(t(target), nbasis(model))
    G0 <- matrix(0, nrow = N, ncol = nbasis(model))
    for (i in 1:N) {
        G0[i, ans$cluster[i]] <- 1
    }
    G0 <- G0 + 0.2
    coef(
Execution halted
BUILD report for DASC on malbec1

Summary

Command output
