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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 NanoTube
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* checking for file ‘NanoTube/DESCRIPTION’ ... OK
* preparing ‘NanoTube’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘NanoTube.Rmd’ using rmarkdown
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

Welcome to Bioconductor

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

Loading required package: ggplot2
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Warning in read_sampleData(dat, file.name = sampleTab, idCol = idCol, groupCol = groupCol,  :
  
idCol not provided. Assuming the first column of 'GSE117751_sample_data.csv' contains sample ID's.

Warning in read_sampleData(dat, file.name = sampleTab, idCol = idCol, groupCol = groupCol,  :
  
Sample names in the two files don't match. NanoTube is
assuming that samples are in the same order. Please confirm
with your data.

Warning in read_sampleData(dat, file.name = sampleTab, idCol = idCol, groupCol = groupCol,  :
  
idCol not provided. Assuming the first column of 'GSE117751_sample_data.csv' contains sample ID's.

Warning in read_sampleData(dat, file.name = sampleTab, idCol = idCol, groupCol = groupCol,  :
  
Sample names in the two files don't match. NanoTube is
assuming that samples are in the same order. Please confirm
with your data.


Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

The operation couldn’t be completed. Unable to locate a Java Runtime.
Please visit http://www.java.com for information on installing Java.

Quitting from lines 627-634 (NanoTube.Rmd) 
Error: processing vignette 'NanoTube.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'rJava', details:
  call: fun(libname, pkgname)
  error: JVM could not be found
--- failed re-building ‘NanoTube.Rmd’

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

Error: Vignette re-building failed.
Execution halted