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BioC 3.5: CHECK report for ballgown on malbec2

This page was generated on 2017-10-18 14:16:02 -0400 (Wed, 18 Oct 2017).

Package 83/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ballgown 2.8.4
Jack Fu
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/ballgown
Branch: RELEASE_3_5
Last Commit: 4ba7765
Last Changed Date: 2017-07-29 12:33:00 -0400 (Sat, 29 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 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
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ballgown
Version: 2.8.4
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ballgown_2.8.4.tar.gz
StartedAt: 2017-10-17 21:20:02 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 21:23:41 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 219.1 seconds
RetCode: 0
Status:  OK 
CheckDir: ballgown.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ballgown_2.8.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ballgown.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘2.8.4’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.5-bioc/meat/ballgown.Rcheck/00check.log’
for details.


ballgown.Rcheck/00install.out:

* installing *source* package ‘ballgown’ ...
** R
** data
** inst
** preparing 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
* DONE (ballgown)

ballgown.Rcheck/ballgown-Ex.timings:

nameusersystemelapsed
annotate_assembly3.0080.0123.023
ballgown-class0.2000.0000.201
ballgown-constructor0.3760.0080.385
ballgownrsem2.6120.0362.650
bg0.0280.0000.030
checkAssembledTx000
clusterTranscripts0.1480.0000.152
collapseTranscripts0.2560.0000.257
dirs0.0280.0000.029
eexpr0.0560.0000.053
expr-replace0.0360.0000.034
expr0.0280.0000.030
exprfilter0.0560.0000.053
geneIDs0.0280.0000.029
geneNames0.8920.0040.895
getAttributeField1.1840.0001.186
getGenes0.7360.0000.736
gexpr0.1200.0000.122
gffRead0.2240.0000.225
gffReadGR0.2720.0000.272
iexpr0.0520.0000.051
indexes-replace0.0280.0000.031
indexes0.0320.0000.032
last0.0000.0000.001
mergedDate0.0320.0000.031
pData-replace0.0320.0000.032
pData0.0320.0000.032
pctOverlap0.3440.0000.348
plotLatentTranscripts000
plotMeans000
plotTranscripts000
sampleNames0.0320.0040.036
seqnames0.0280.0000.030
stattest0.2080.0000.208
structure0.0840.0000.087
subset0.1480.0000.150
tGene0.0560.0000.054
texpr0.0320.0000.032
transcriptIDs0.0320.0000.032
transcriptNames0.0320.0000.033
writeFiles000