launcher.r.Rout

R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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> 
> library(shiny)
Warning message:
package 'shiny' was built under R version 3.2.3 
> 
> runApp("C:\\Users\\Sili Fan\\Desktop\\WORK\\WCMC\\tools\\DeviumWeb", port=4444) # work
Loading required package: plotly
Loading required package: ggplot2
Warning: package 'ggplot2' was built under R version 3.2.3

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

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

    layout

Loading required package: knitr
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula

Attaching package: 'Hmisc'

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

    subplot

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

    format.pval, round.POSIXt, trunc.POSIXt, units

Loading required package: car
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
Loading required package: tools
Loading required package: gridExtra
Loading required package: markdown
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.0 (2015-02-19) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.19.0 (2015-02-27) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object is masked _by_ '.GlobalEnv':

    trim

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

    printStackTrace

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

    getClasses, getMethods

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

    attach, detach, gc, load, save

R.utils v2.2.0 (2015-12-09) successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

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

    capitalize

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

    setProgress, validate

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

    timestamp

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

    cat, commandArgs, getOption, inherits, isOpen, parse, warnings

Loading required package: psych

Attaching package: 'psych'

The following object is masked _by_ '.GlobalEnv':

    rescale

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

    logit

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

    describe

The following objects are masked from 'package:ggplot2':

    %+%, alpha

Loading required package: rela
Loading required package: plyr

Attaching package: 'plyr'

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    ., rename

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

    is.discrete, summarize

Loading required package: reshape2
Loading required package: vegan
Loading required package: permute

Attaching package: 'permute'

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    check

This is vegan 2.3-3
Loading required package: lubridate

Attaching package: 'lubridate'

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    here

Loading required package: pander

Attaching package: 'pander'

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    wrap

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    p

Loading required package: wordcloud
Loading required package: RColorBrewer
Loading required package: impute
Loading required package: WGCNA
Loading required package: dynamicTreeCut
Loading required package: fastcluster

Attaching package: 'fastcluster'

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

    hclust

Note: the specification for S3 class "AsIs" in package 'BiocGenerics' seems equivalent to one from package 'jsonlite': not turning on duplicate class definitions for this class.
Loading required package: DBI

==========================================================================
*
*  Package WGCNA 1.49 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=8
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=8
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================



Attaching package: 'WGCNA'

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

    cor

Loading required package: RJSONIO
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'jsonlite': not turning on duplicate class definitions for this class.
Loading required package: pwr
Loading required package: AER
Loading required package: lmtest
Loading required package: zoo

Attaching package: 'zoo'

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    as.Date, as.Date.numeric


Attaching package: 'lmtest'

The following object is masked from 'package:R.utils':

    reset

Loading required package: sandwich
Loading required package: Ecdat
Loading required package: Ecfun

Attaching package: 'Ecdat'

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    Mroz

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

    Orange

Loading required package: foreign
Loading required package: xts
Loading required package: fdrtool
Loading required package: pls

Attaching package: 'pls'

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

    scores

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

    loadings

Loading required package: qvalue

Attaching package: 'qvalue'

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

    qvalue

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:lubridate':

    intersect, setdiff, union

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

    combine

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

    IQR, mad, xtabs

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

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
    do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unlist, unsplit

Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    contents


Attaching package: 'pcaMethods'

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    loadings, scores

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

    scores

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

    loadings

Loading required package: hexbin
Loading required package: shinyBS
Loading required package: httr

Attaching package: 'httr'

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

    content

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

    config

Loading required package: jsonlite

Attaching package: 'jsonlite'

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

    fromJSON, toJSON

The following object is masked from 'package:R.utils':

    validate

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

    validate

Loading required package: Rcpp
Loading required package: shinybootstrap2
You probably do not want to attach this package (with library() or require()). Instead, you should use shinybootstrap2::withBootstrap2(). You can hide this message with suppressPackageStartupMessages().

Attaching package: 'shinybootstrap2'

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

    animationOptions, basicPage, bootstrapPage, checkboxGroupInput,
    checkboxInput, column, dataTableOutput, dateInput, dateRangeInput,
    fixedPage, fixedRow, fluidPage, fluidRow, headerPanel, icon,
    mainPanel, navbarPage, navlistPanel, numericInput, pageWithSidebar,
    radioButtons, selectInput, selectizeInput, sidebarLayout,
    sidebarPanel, sliderInput, submitButton, textInput, titlePanel,
    updateCheckboxGroupInput, updateRadioButtons, updateSliderInput,
    verticalLayout


Listening on http://127.0.0.1:4444
Error in startServer(host, port, handlerManager$createHttpuvApp()) : 
  Failed to create server
Calls: runApp -> startApp -> startServer
Execution halted