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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BioMM
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* checking for file ‘BioMM/DESCRIPTION’ ... OK
* preparing ‘BioMM’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘BioMMtutorial.Rmd’ using rmarkdown
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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    latex

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

    format.pval, units

Loading required package: SparseM

Attaching package: 'SparseM'

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    backsolve

Loading required package: Matrix
Loaded glmnet 4.1-4

Attaching package: 'e1071'

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

    impute

Loading required package: sm
Package 'sm', version 2.2-5.7: type help(sm) for summary information
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Much appreciate for using CMplot.
Full description, Bug report, Suggestion and the latest codes:
https://github.com/YinLiLin/CMplot
Loading required package: magrittr

Attaching package: 'imager'

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    add

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    label

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

    convolve, spectrum

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    frame

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    save.image

Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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    width

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, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which.max, which.min

Loading required package: graph

Attaching package: 'graph'

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    boundary, threshold

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")'.


Attaching package: 'Biobase'

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    channel

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    contents

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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    expand, unname

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    I, expand.grid, unname


Attaching package: 'IRanges'

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    resize



groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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    members

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Warning in fun(libname, pkgname) :
  JAVA_HOME is set incorrectly! Ingoring.
The operation couldn’t be completed. Unable to locate a Java Runtime.
Please visit http://www.java.com for information on installing Java.

Warning in system("/usr/libexec/java_home", intern = TRUE) :
  running command '/usr/libexec/java_home' had status 1
Warning in fun(libname, pkgname) :
  Cannot find JVM library 'NA/lib/server/libjvm.dylib'
Install Java and/or check JAVA_HOME (if in doubt, do NOT set it, it will be detected)
Quitting from lines 68-80 (BioMMtutorial.Rmd) 
Error: processing vignette 'BioMMtutorial.Rmd' failed with diagnostics:
package or namespace load failed for 'xlsx':
 .onLoad failed in loadNamespace() for 'rJava', details:
  call: fun(libname, pkgname)
  error: JVM could not be found
--- failed re-building ‘BioMMtutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘BioMMtutorial.Rmd’

Error: Vignette re-building failed.
Execution halted