Package: ballgown

Version: 2.19.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ballgown.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ballgown_2.19.0.tar.gz

StartedAt: 2020-01-16 01:54:30 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 02:05:56 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 686.2 seconds

RetCode: 0

Status:  OK

CheckDir: ballgown.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ballgown.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ballgown_2.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/ballgown.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ballgown/DESCRIPTION’ ... OK
* this is package ‘ballgown’ version ‘2.19.0’
* 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 : <anonymous>: 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 (user + system) or elapsed time > 5s
                   user system elapsed
annotate_assembly 50.52  0.591  55.094
* 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-3.11-bioc/meat/ballgown.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ballgown
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 141 | SKIPPED: 0 | WARNINGS: 39 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
220.015   3.564 229.306 

name	user	system	elapsed
annotate_assembly	50.520	0.591	55.094
ballgown-class	0.105	0.012	0.117
ballgown-constructor	0.363	0.043	0.444
ballgownrsem	3.908	0.099	4.114
bg	0.052	0.006	0.057
checkAssembledTx	0.000	0.000	0.001
clusterTranscripts	0.765	0.039	0.805
collapseTranscripts	0.798	0.015	0.814
dirs	0.042	0.006	0.049
eexpr	0.047	0.006	0.054
expr-replace	0.045	0.006	0.051
expr	0.041	0.007	0.048
exprfilter	0.123	0.019	0.142
geneIDs	0.044	0.010	0.053
geneNames	2.880	0.106	2.987
getAttributeField	2.480	0.014	2.498
getGenes	2.572	0.023	2.599
gexpr	2.168	0.015	2.188
gffRead	0.162	0.003	0.165
gffReadGR	0.588	0.007	0.597
iexpr	0.048	0.009	0.057
indexes-replace	0.045	0.006	0.051
indexes	0.046	0.007	0.053
last	0.002	0.000	0.002
mergedDate	0.043	0.007	0.050
pData-replace	0.046	0.007	0.054
pData	0.046	0.007	0.053
pctOverlap	0.544	0.011	0.557
plotLatentTranscripts	0.000	0.001	0.000
plotMeans	0.000	0.000	0.001
plotTranscripts	0.001	0.000	0.001
sampleNames	0.041	0.006	0.048
seqnames	0.047	0.008	0.060
stattest	0.141	0.012	0.155
structure	0.071	0.007	0.078
subset	0.468	0.070	0.542
tGene	0.055	0.007	0.062
texpr	0.046	0.007	0.053
transcriptIDs	0.044	0.008	0.052
transcriptNames	0.048	0.009	0.057
writeFiles	0	0	0