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BioC 3.4: CHECK report for ballgown on morelia

This page was generated on 2017-04-15 16:25:42 -0400 (Sat, 15 Apr 2017).

Package 81/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ballgown 2.6.0
Jack Fu
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ballgown
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ballgown
Version: 2.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ballgown_2.6.0.tar.gz
StartedAt: 2017-04-14 22:51:53 -0700 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:56:19 -0700 (Fri, 14 Apr 2017)
EllapsedTime: 265.7 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_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ballgown.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.6.0’
* 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 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-3.4-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_assembly3.3250.0393.374
ballgown-class0.0730.0070.080
ballgown-constructor0.5030.0110.515
ballgownrsem3.5460.0603.613
bg0.0350.0070.042
checkAssembledTx000
clusterTranscripts0.1490.0070.156
collapseTranscripts0.5630.0100.574
contains1.4970.0211.521
dirs0.0330.0070.040
eexpr0.0400.0080.049
expr-replace0.0460.0080.054
expr0.0380.0070.046
exprfilter0.0700.0090.079
geneIDs0.0320.0070.040
geneNames0.3250.0130.339
getAttributeField1.4910.0071.499
getGenes0.2860.0120.297
gexpr0.1240.0090.133
gffRead0.2710.0000.271
gffReadGR0.3310.0080.340
iexpr0.0370.0070.045
indexes-replace0.0330.0070.040
indexes0.0300.0060.037
last0.0010.0000.001
mergedDate0.0330.0080.041
pData-replace0.0380.0090.048
pData0.0380.0090.047
pctOverlap0.3320.0130.347
plotLatentTranscripts0.0000.0000.001
plotMeans0.0000.0000.001
plotTranscripts000
sampleNames0.0370.0070.044
seqnames0.0340.0080.042
stattest0.0930.0080.100
structure0.0480.0080.056
subset0.1140.0080.122
tGene0.0370.0070.044
texpr0.0360.0080.045
transcriptIDs0.0360.0080.044
transcriptNames0.0490.0090.059
writeFiles0.0000.0010.001