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BioC 3.3: CHECK report for ballgown on oaxaca

This page was generated on 2016-10-13 13:00:34 -0700 (Thu, 13 Oct 2016).

Package 74/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ballgown 2.4.3
Jack Fu
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/ballgown
Last Changed Rev: 121808 / Revision: 122332
Last Changed Date: 2016-10-05 05:54:37 -0700 (Wed, 05 Oct 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ballgown
Version: 2.4.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ballgown_2.4.3.tar.gz
StartedAt: 2016-10-12 23:25:32 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:29:39 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 246.4 seconds
RetCode: 0
Status:  OK 
CheckDir: ballgown.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ballgown_2.4.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ballgown.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ballgown/DESCRIPTION’ ... OK
* this is package ‘ballgown’ version ‘2.4.3’
* 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
  ‘/Users/biocbuild/bbs-3.3-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_assembly3.1890.0303.227
ballgown-class0.0650.0060.071
ballgown-constructor0.4720.0110.484
ballgownrsem3.7710.0643.845
bg0.0380.0100.048
checkAssembledTx0.0010.0000.000
clusterTranscripts0.1620.0100.171
collapseTranscripts0.2520.0100.262
contains1.8040.0311.841
dirs0.0370.0090.047
eexpr0.0330.0070.040
expr-replace0.0400.0070.047
expr0.0320.0080.040
exprfilter0.0680.0100.078
geneIDs0.0390.0090.048
geneNames0.3150.0130.329
getAttributeField1.5550.0071.565
getGenes0.3110.0120.324
gexpr0.1060.0090.116
gffRead0.3380.0010.339
gffReadGR0.3840.0050.389
iexpr0.0370.0080.045
indexes-replace0.0350.0100.044
indexes0.0370.0080.045
last0.0010.0000.001
mergedDate0.0310.0090.039
pData-replace0.0370.0080.044
pData0.0380.0090.046
pctOverlap0.3210.0090.331
plotLatentTranscripts0.0000.0000.001
plotMeans0.0000.0000.001
plotTranscripts0.0010.0000.001
sampleNames0.0330.0080.041
seqnames0.0320.0070.039
stattest0.1070.0130.121
structure0.0460.0080.055
subset0.1120.0090.121
tGene0.0390.0070.046
texpr0.0350.0080.042
transcriptIDs0.0360.0090.045
transcriptNames0.0340.0070.041
writeFiles0.0010.0000.001