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CHECK report for ballgown on malbec2

This page was generated on 2019-10-16 12:04:57 -0400 (Wed, 16 Oct 2019).

Package 101/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ballgown 2.16.0
Jack Fu
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ballgown
Branch: RELEASE_3_9
Last Commit: 9113480
Last Changed Date: 2019-05-02 11:53:48 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ballgown
Version: 2.16.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ballgown.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ballgown_2.16.0.tar.gz
StartedAt: 2019-10-15 23:53:59 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-16 00:00:25 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 385.7 seconds
RetCode: 0
Status:  OK 
CheckDir: ballgown.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ballgown.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ballgown_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ballgown.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ballgown/DESCRIPTION’ ... OK
* this is package ‘ballgown’ version ‘2.16.0’
* 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 : : no visible global function definition for
  ‘read.table’
checkAssembledTx: no visible global function definition for ‘par’
checkAssembledTx: no visible global function definition for ‘plot’
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 ‘plot’
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 ‘plot’
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 plot polygon read.table t_id text
  title write.table
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "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 or elapsed time > 5s
                    user system elapsed
annotate_assembly 28.278  0.159  28.672
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/ballgown.Rcheck/00check.log’
for details.



Installation output

ballgown.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ballgown
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 141 | SKIPPED: 0 | WARNINGS: 39 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
105.312   0.688 106.101 

Example timings

ballgown.Rcheck/ballgown-Ex.timings

nameusersystemelapsed
annotate_assembly28.278 0.15928.672
ballgown-class0.0690.0000.069
ballgown-constructor0.2500.0080.357
ballgownrsem2.4340.0323.065
bg0.0450.0000.044
checkAssembledTx000
clusterTranscripts0.3980.0070.413
collapseTranscripts0.3840.0000.391
dirs0.0640.0000.064
eexpr0.0440.0000.044
expr-replace0.0460.0000.046
expr0.0410.0000.041
exprfilter0.0600.0000.061
geneIDs0.0420.0000.042
geneNames0.4530.0000.453
getAttributeField1.2930.0001.294
getGenes0.3350.0040.339
gexpr0.1130.0040.117
gffRead0.1560.0000.157
gffReadGR0.4120.0000.413
iexpr0.0380.0040.042
indexes-replace0.0530.0040.057
indexes0.0280.0040.031
last000
mergedDate0.0280.0000.028
pData-replace0.0290.0000.029
pData0.0280.0000.028
pctOverlap0.2350.0000.235
plotLatentTranscripts000
plotMeans0.0010.0000.000
plotTranscripts000
sampleNames0.0410.0000.041
seqnames0.0410.0000.041
stattest0.0960.0000.096
structure0.0510.0000.051
subset0.1870.0000.187
tGene0.0420.0040.046
texpr0.0410.0000.041
transcriptIDs0.0420.0000.042
transcriptNames0.0440.0000.044
writeFiles000