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BioC 3.5: CHECK report for ballgown on tokay2

This page was generated on 2017-08-16 13:23:31 -0400 (Wed, 16 Aug 2017).

Package 83/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ballgown 2.8.4
Jack Fu
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ballgown
Last Changed Rev: 131651 / Revision: 131943
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: rm -rf ballgown.buildbin-libdir ballgown.Rcheck && mkdir ballgown.buildbin-libdir ballgown.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ballgown.buildbin-libdir ballgown_2.8.4.tar.gz >ballgown.Rcheck\00install.out 2>&1 && cp ballgown.Rcheck\00install.out ballgown-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ballgown.buildbin-libdir --install="check:ballgown-install.out" --force-multiarch --no-vignettes --timings ballgown_2.8.4.tar.gz
StartedAt: 2017-08-15 22:06:45 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:13:04 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 378.8 seconds
RetCode: 0
Status:  OK  
CheckDir: ballgown.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ballgown.buildbin-libdir ballgown.Rcheck && mkdir ballgown.buildbin-libdir ballgown.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ballgown.buildbin-libdir ballgown_2.8.4.tar.gz >ballgown.Rcheck\00install.out 2>&1 && cp ballgown.Rcheck\00install.out ballgown-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ballgown.buildbin-libdir --install="check:ballgown-install.out" --force-multiarch --no-vignettes --timings ballgown_2.8.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ballgown.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/ballgown.Rcheck/00check.log'
for details.


ballgown.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'ballgown' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ballgown' as ballgown_2.8.4.zip
* DONE (ballgown)

ballgown.Rcheck/examples_i386/ballgown-Ex.timings:

nameusersystemelapsed
annotate_assembly2.790.082.91
ballgown-class0.100.000.09
ballgown-constructor0.360.030.39
ballgownrsem3.020.013.03
bg0.030.020.05
checkAssembledTx000
clusterTranscripts0.160.020.17
collapseTranscripts0.390.000.39
dirs0.040.010.06
eexpr0.10.00.1
expr-replace0.030.020.04
expr0.030.010.05
exprfilter0.060.020.08
geneIDs0.050.000.05
geneNames1.170.001.17
getAttributeField1.440.031.47
getGenes0.310.010.33
gexpr0.130.020.14
gffRead0.250.000.25
gffReadGR0.560.000.56
iexpr0.080.000.08
indexes-replace0.030.030.06
indexes0.10.00.1
last000
mergedDate0.070.000.08
pData-replace0.080.000.07
pData0.070.000.07
pctOverlap0.540.000.54
plotLatentTranscripts000
plotMeans000
plotTranscripts000
sampleNames0.030.000.03
seqnames0.060.030.09
stattest0.310.000.32
structure0.130.000.12
subset0.170.000.17
tGene0.060.000.07
texpr0.030.020.04
transcriptIDs0.030.000.03
transcriptNames0.050.000.05
writeFiles000

ballgown.Rcheck/examples_x64/ballgown-Ex.timings:

nameusersystemelapsed
annotate_assembly3.780.033.81
ballgown-class0.110.000.11
ballgown-constructor0.40.00.4
ballgownrsem3.350.063.41
bg0.050.000.05
checkAssembledTx000
clusterTranscripts0.280.000.28
collapseTranscripts0.390.020.41
dirs0.050.000.05
eexpr0.080.010.09
expr-replace0.040.000.05
expr0.050.000.04
exprfilter0.060.000.07
geneIDs0.030.000.03
geneNames1.200.001.21
getAttributeField2.410.002.40
getGenes0.410.000.41
gexpr0.260.020.28
gffRead0.470.000.47
gffReadGR0.660.000.65
iexpr0.060.030.10
indexes-replace0.050.010.06
indexes0.040.000.05
last000
mergedDate0.050.000.04
pData-replace0.050.000.05
pData0.040.000.04
pctOverlap0.770.000.76
plotLatentTranscripts000
plotMeans000
plotTranscripts000
sampleNames0.040.000.05
seqnames0.050.000.04
stattest0.370.030.41
structure0.180.000.17
subset0.280.000.28
tGene0.090.000.10
texpr0.050.010.06
transcriptIDs0.040.000.05
transcriptNames0.050.020.06
writeFiles000