Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-25 14:06:49 -0400 (Mon, 25 Oct 2021).

CHECK results for ballgown on merida1

To the developers/maintainers of the ballgown package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ballgown.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 109/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ballgown 2.25.1  (landing page)
Jack Fu
Snapshot Date: 2021-10-24 14:50:04 -0400 (Sun, 24 Oct 2021)
git_url: https://git.bioconductor.org/packages/ballgown
git_branch: master
git_last_commit: 0d2092f
git_last_commit_date: 2021-08-29 21:19:12 -0400 (Sun, 29 Aug 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  

Summary

Package: ballgown
Version: 2.25.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ballgown.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ballgown_2.25.1.tar.gz
StartedAt: 2021-10-25 00:45:27 -0400 (Mon, 25 Oct 2021)
EndedAt: 2021-10-25 00:55:10 -0400 (Mon, 25 Oct 2021)
EllapsedTime: 583.1 seconds
RetCode: 0
Status:   OK  
CheckDir: ballgown.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ballgown.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ballgown_2.25.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ballgown.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ballgown/DESCRIPTION’ ... OK
* this is package ‘ballgown’ version ‘2.25.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ballgown’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.readExon: no visible global function definition for ‘read.table’
.readIntron: no visible global function definition for ‘read.table’
.readTranscript: no visible global function definition for ‘read.table’
assessSim: no visible global function definition for ‘read.table’
assessSim: no visible global function definition for ‘lines’
assessSim: no visible global function definition for ‘legend’
ballgown: no visible global function definition for ‘read.table’
ballgownrsem: no visible global function definition for ‘read.table’
ballgownrsem : <anonymous>: no visible global function definition for
  ‘read.table’
checkAssembledTx: no visible global function definition for ‘par’
checkAssembledTx: no visible global function definition for ‘polygon’
checkAssembledTx: no visible global function definition for ‘lines’
checkAssembledTx: no visible global function definition for ‘abline’
checkAssembledTx: no visible global function definition for ‘title’
checkAssembledTx: no visible global function definition for ‘axis’
closestColor: no visible global function definition for ‘heat.colors’
clusterTranscripts: no visible global function definition for ‘cutree’
clusterTranscripts: no visible global function definition for ‘hclust’
clusterTranscripts: no visible global function definition for ‘as.dist’
clusterTranscripts: no visible global function definition for ‘kmeans’
gffRead: no visible global function definition for ‘read.table’
plotMeans: no visible global function definition for ‘par’
plotMeans: no visible global function definition for ‘polygon’
plotMeans: no visible global function definition for ‘lines’
plotMeans: no visible global function definition for ‘heat.colors’
plotMeans: no visible global function definition for ‘text’
plotMeans: no visible global function definition for ‘axis’
plotTranscripts: no visible global function definition for ‘par’
plotTranscripts: no visible global function definition for ‘title’
plotTranscripts: no visible global function definition for ‘polygon’
plotTranscripts: no visible global function definition for ‘lines’
plotTranscripts: no visible global function definition for
  ‘heat.colors’
plotTranscripts: no visible global function definition for ‘text’
plotTranscripts: no visible global function definition for ‘axis’
stattest: no visible global function definition for ‘model.matrix’
stattest: no visible global function definition for ‘p.adjust’
writeFiles: no visible global function definition for ‘write.table’
subset,ballgown: no visible binding for global variable ‘i_id’
subset,ballgown: no visible binding for global variable ‘e_id’
subset,ballgown: no visible binding for global variable ‘t_id’
Undefined global functions or variables:
  abline as.dist axis cutree e_id hclust heat.colors i_id kmeans legend
  lines model.matrix p.adjust par polygon read.table t_id text title
  write.table
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "polygon", "text", "title")
  importFrom("stats", "as.dist", "cutree", "hclust", "kmeans",
             "model.matrix", "p.adjust")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
annotate_assembly 38.066  0.258  38.372
contains          19.074  0.069  19.178
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/ballgown.Rcheck/00check.log’
for details.



Installation output

ballgown.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ballgown
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘ballgown’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘structure’ in package ‘ballgown’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ballgown)

Tests output

ballgown.Rcheck/tests/test-all.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check('ballgown')
Loading required package: ballgown

Attaching package: 'ballgown'

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

    structure

[ FAIL 0 | WARN 34 | SKIP 0 | PASS 132 ]
> 
> proc.time()
   user  system elapsed 
162.082   1.467 163.685 

Example timings

ballgown.Rcheck/ballgown-Ex.timings

nameusersystemelapsed
annotate_assembly38.066 0.25838.372
ballgown-class0.1090.0020.112
ballgown-constructor0.3110.0270.350
ballgownrsem3.1750.0283.208
bg0.0600.0020.063
checkAssembledTx000
clusterTranscripts0.5200.0030.524
collapseTranscripts0.6480.0090.658
contains19.074 0.06919.178
dirs0.0430.0030.046
eexpr0.0480.0020.050
expr-replace0.0530.0020.055
expr0.0410.0010.042
exprfilter0.1170.0020.120
geneIDs0.0430.0020.045
geneNames3.0850.0113.100
getAttributeField1.4720.0061.479
getGenes2.9460.0092.958
gexpr2.5730.0072.582
gffRead0.1550.0010.156
gffReadGR0.5340.0030.537
iexpr0.0430.0020.045
indexes-replace0.0370.0020.039
indexes0.0430.0010.046
last0.0010.0000.001
mergedDate0.0450.0020.048
pData-replace0.0450.0030.047
pData0.0480.0020.049
pctOverlap0.5070.0060.513
plotLatentTranscripts0.0000.0000.001
plotMeans000
plotTranscripts000
sampleNames0.0420.0020.044
seqnames0.0420.0030.044
stattest0.1210.0040.125
structure0.0740.0020.077
subset0.3340.0030.337
tGene0.0520.0020.056
texpr0.0480.0020.050
transcriptIDs0.0440.0020.046
transcriptNames0.0470.0030.050
writeFiles000