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BioC 3.5: BUILD report for ChAMP on veracruz2

This page was generated on 2017-10-18 14:31:31 -0400 (Wed, 18 Oct 2017).

Package 198/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChAMP 2.8.9
Yuan Tian
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/ChAMP
Branch: RELEASE_3_5
Last Commit: 517c3c0
Last Changed Date: 2017-10-08 18:07:15 -0400 (Sun, 08 Oct 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  ERROR  skipped  skipped 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded [ ERROR ] skipped  skipped 

Summary

Package: ChAMP
Version: 2.8.9
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ChAMP
StartedAt: 2017-10-17 20:34:06 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 20:35:22 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 75.9 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ChAMP
###
##############################################################################
##############################################################################


* checking for file ‘ChAMP/DESCRIPTION’ ... OK
* preparing ‘ChAMP’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: minfi
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

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

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:base':

    apply

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    type

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

    strsplit

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: ChAMPdata
Loading required package: FEM
Loading required package: AnnotationDbi
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: marray
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: corrplot
corrplot 0.84 loaded
Loading required package: igraph

Attaching package: 'igraph'

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

    union

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

    union

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

    union

The following object is masked from 'package:S4Vectors':

    union

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: impute
Loading required package: org.Hs.eg.db

Loading required package: graph

Attaching package: 'graph'

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

    degree, edges, intersection

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

    complement

Warning: replacing previous import 'igraph::edges' by 'graph::edges' when loading 'FEM'
Warning: replacing previous import 'igraph::intersection' by 'graph::intersection' when loading 'FEM'
Warning: replacing previous import 'igraph::degree' by 'graph::degree' when loading 'FEM'
Warning: replacing previous import 'igraph::union' by 'graph::union' when loading 'FEM'
Warning: replacing previous import 'limma::plotMA' by 'BiocGenerics::plotMA' when loading 'FEM'
Warning: replacing previous import 'Matrix::colSums' by 'BiocGenerics::colSums' when loading 'FEM'
Warning: replacing previous import 'Matrix::colMeans' by 'BiocGenerics::colMeans' when loading 'FEM'
Warning: replacing previous import 'Matrix::rowMeans' by 'BiocGenerics::rowMeans' when loading 'FEM'
Warning: replacing previous import 'Matrix::rowSums' by 'BiocGenerics::rowSums' when loading 'FEM'
Warning: replacing previous import 'Matrix::which' by 'BiocGenerics::which' when loading 'FEM'
Warning: replacing previous import 'igraph::normalize' by 'BiocGenerics::normalize' when loading 'FEM'
Loading required package: DMRcate
Loading required package: DSS
Loading required package: bsseq

Attaching package: 'bsseq'

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

    getMeth

Loading required package: splines
Loading required package: DMRcatedata

Loading required package: Illumina450ProbeVariants.db
Loading required package: IlluminaHumanMethylationEPICmanifest
Warning: replacing previous import 'plyr::summarise' by 'plotly::summarise' when loading 'ChAMP'
Warning: replacing previous import 'plyr::rename' by 'plotly::rename' when loading 'ChAMP'
Warning: replacing previous import 'plyr::arrange' by 'plotly::arrange' when loading 'ChAMP'
Warning: replacing previous import 'plyr::mutate' by 'plotly::mutate' when loading 'ChAMP'
>> Package version 2.8.9 loaded <<
       ___ _      _   __  __ ___ 
      / __| |_   /_\ |  \/  | _ \
     | (__| ' \ / _ \| |\/| |  _/
      \___|_||_/_/ \_\_|  |_|_|  
      ------------------------------
--- 1: ChAMP provides comprehensive integrated analysis pipeline for DNA methylation HumanMethylation Beadchip.
--- 2: You may use vignette("ChAMP") to view html version guildbook.
--- 3: If you have any question or suggestion about ChAMP, please email to champ450k@gmail.com.
[===========================]
[<<<<< ChAMP.QC START >>>>>>]
-----------------------------
champ.QC Results will be saved in ./CHAMP_QCimages/
[QC plots will be proceed with 425783 probes and 8 samples.]

<< Prepare Data Over. >>
<< plot mdsPlot Done. >>

<< Plot densityPlot Done. >>

< Dendrogram Plot Feature Selection Method >: No Selection, directly use all CpGs to calculate distance matrix.
<< Plot dendrogram Done. >>

[<<<<<< ChAMP.QC END >>>>>>>]
[===========================]
[You may want to process champ.norm() next.]

[===========================]
[<<<<< ChAMP.DMP START >>>>>]
-----------------------------
!!! Important !!! New Modification has been made on champ.DMP(): 

    (1): In this version champ.DMP() if your pheno parameter contains more than two groups of phenotypes, champ.DMP() would do pairewise differential methylated analysis between each pair of them. But you can also specify compare.group to only do comparasion between any two of them.

    (2): champ.DMP() now support numeric as pheno, and will do linear regression on them. So covariates like age could be inputted in this function. You need to make sure your inputted "pheno" parameter is "numeric" type.

--------------------------------

[ Section 1:  Check Input Pheno Start ]

  You pheno is character type.
    Your pheno information contains following groups. >>
    <C>:4 samples.
    <T>:4 samples.
    [The power of statistics analysis on groups contain very few samples may not strong.]
    pheno contains only 2 phenotypes
    compare.group parameter is NULL, two pheno types will be added into Compare List.
    C_to_T compare group : C, T

[ Section 1:  Check Input Pheno Done ]


[ Section 2:  Find Differential Methylated CpGs Start ]

  -----------------------------
  Start to Compare : C, T
  Contrast Matrix
  You have found 4058 significant MVPs with a BH adjusted P-value below 0.05.
  Calculate DMP for C and T done.

[ Section 2:  Find Numeric Vector Related CpGs Done ]


[ Section 3:  Match Annotation Start ]


[ Section 3:  Match Annotation Done ]

[<<<<<< ChAMP.DMP END >>>>>>]
[===========================]
[You may want to process DMP.GUI() or champ.GSEA() next.]

pandoc: Could not fetch https://fonts.googleapis.com/css?family=Merriweather:400,700
TlsExceptionHostPort (HandshakeFailed Error_EOF) "fonts.googleapis.com" 443
Error: processing vignette 'ChAMP.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted