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BUILD report for DASC on malbec1

This page was generated on 2018-04-12 13:16:17 -0400 (Thu, 12 Apr 2018).

Package 332/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DASC 1.0.0
Haidong Yi
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/DASC
Branch: RELEASE_3_6
Last Commit: ba52a72
Last Changed Date: 2017-10-30 12:41:29 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded [ ERROR ] skipped 
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: DASC
Version: 1.0.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data DASC
StartedAt: 2018-04-11 20:57:35 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 20:58:22 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 46.9 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data DASC
###
##############################################################################
##############################################################################


* 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