ChAMP 2.9.9
Yuan Tian
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ChAMP | | Last Changed Rev: 131850 / Revision: 131943 | | Last Changed Date: 2017-08-08 11:29:37 -0400 (Tue, 08 Aug 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | [ ERROR ] | skipped | skipped | |
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | WARNINGS | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### chmod a+r ChAMP -R && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe 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 ...Warning: running command '"C:/Users/biocbuild/bbs-3.6-bioc/R/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
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
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 2.9.9 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.exe: Could not fetch https://fonts.googleapis.com/css?family=Merriweather:400,700
HttpExceptionRequest Request {
host = "fonts.googleapis.com"
port = 443
secure = True
requestHeaders = []
path = "/css"
queryString = "?family=Merriweather:400,700"
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
}
(ConnectionFailure <socket: 600>: hPutBuf: failed (Unknown error))
Warning: running command '"C:/PROGRA˜2/Pandoc/pandoc" +RTS -K512m -RTS ChAMP.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output ChAMP.html --smart --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 3 --template "C:\Users\biocbuild\bbs-3.6-bioc\R\library\rmarkdown\rmd\h\default.html" --highlight-style pygments --number-sections --css ChAMP.css --id-prefix section- --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" --include-in-header "C:\Users\biocbuild\bbs-3.6-bioc\tmpdir\RtmpCMOsWe\Rbuildf602ece3ed\ChAMP\vignettes\header.html" --bibliography ChAMP.bib --filter pandoc-citeproc' had status 67
Error: processing vignette 'ChAMP.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted