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This page was generated on 2022-07-07 11:11:36 -0400 (Thu, 07 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4148
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4160
kjohnsonmacOS 12.4 Montereyarm644.2.0 Patched (2022-06-09 r82473) -- "Vigorous Calisthenics" 3115
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD results for NanoTube on kjohnson


To the developers/maintainers of the NanoTube package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/NanoTube.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1293/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
NanoTube 1.3.6  (landing page)
Caleb Class
Snapshot Date: 2022-07-06 14:00:06 -0400 (Wed, 06 Jul 2022)
git_url: https://git.bioconductor.org/packages/NanoTube
git_branch: master
git_last_commit: 84db14f
git_last_commit_date: 2022-06-17 15:40:18 -0400 (Fri, 17 Jun 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnsonmacOS 12.4 Monterey / arm64  OK    ERROR  skippedskipped

Summary

Package: NanoTube
Version: 1.3.6
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data NanoTube
StartedAt: 2022-07-07 00:57:07 -0400 (Thu, 07 Jul 2022)
EndedAt: 2022-07-07 00:57:32 -0400 (Thu, 07 Jul 2022)
EllapsedTime: 24.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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


* 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