Package: rnaSeqMap

Version: 2.36.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rnaSeqMap_2.36.0.tar.gz

StartedAt: 2018-04-12 08:55:08 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 08:58:25 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 196.4 seconds

RetCode: 0

Status:  OK

CheckDir: rnaSeqMap.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings rnaSeqMap_2.36.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/rnaSeqMap.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rnaSeqMap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rnaSeqMap’ version ‘2.36.0’
* 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 ‘rnaSeqMap’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.chr.convert’ ‘.countz’ ‘.munion’ ‘.tunion’ ‘.wytnij’ ‘getBamData’
  ‘newSeqReads’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.exonCoverage: no visible global function definition for ‘exon.details’
.fillRleList: no visible global function definition for ‘Rle’
.geneCoverage: no visible global function definition for ‘gene.details’
.munion: no visible global function definition for ‘exon.details’
.munion: no visible global function definition for ‘gene.to.exon’
.rsCount: no visible global function definition for ‘gene.details’
.simplePlot: no visible global function definition for ‘plot’
.simplePlot: no visible global function definition for ‘lines’
.tunion: no visible global function definition for ‘exon.details’
.tunion: no visible global function definition for ‘transcript.to.exon’
addBamData: no visible global function definition for ‘phenoData’
addBamData: no visible global function definition for ‘phenoData<-’
averageND: no visible global function definition for ‘Rle’
bam2sig: no visible global function definition for ‘dbGetQuery’
bam2sig: no visible global function definition for ‘read.table’
combineND: no visible global function definition for ‘Rle’
distrCOVPlot: no visible global function definition for ‘topo.colors’
distrCOVPlot: no visible global function definition for ‘par’
distrCOVPlot: no visible global function definition for ‘plot’
distrCOVPlot: no visible global function definition for ‘lines’
distrCOVPlot: no visible global function definition for ‘legend’
distrCOVPlot: no visible global function definition for ‘gene.details’
distrCOVPlot: no visible global function definition for
  ‘gene.to.transcript’
distrCOVPlot: no visible global function definition for ‘exon.details’
distrCOVPlot: no visible global function definition for
  ‘transcript.to.exon’
distrCOVPlot: no visible global function definition for ‘rect’
distrCOVPlotg: no visible global function definition for ‘topo.colors’
distrCOVPlotg: no visible global function definition for ‘par’
distrCOVPlotg: no visible global function definition for ‘gene.details’
distrCOVPlotg: no visible global function definition for ‘exon.details’
distrCOVPlotg: no visible global function definition for ‘gene.to.exon’
distrCOVPlotg: no visible global function definition for ‘plot’
distrCOVPlotg: no visible global function definition for ‘lines’
distrCOVPlotg: no visible global function definition for ‘legend’
distrCOVPlotg: no visible global function definition for
  ‘gene.to.transcript’
distrCOVPlotg: no visible global function definition for
  ‘transcript.to.exon’
distrCOVPlotg: no visible global function definition for ‘rect’
distrSIPlot: no visible global function definition for ‘par’
distrSIPlot: no visible global function definition for ‘plot’
distrSIPlot: no visible global function definition for ‘lines’
distrSIPlot: no visible global function definition for ‘legend’
generatorAdd: no visible global function definition for ‘Rle’
generatorAddSquare: no visible global function definition for ‘Rle’
generatorMultiply: no visible global function definition for ‘Rle’
generatorPeak: no visible global function definition for ‘Rle’
generatorSynth: no visible global function definition for ‘Rle’
getBamData: no visible global function definition for ‘read.table’
getCoverageFromRS: no visible global function definition for
  ‘phenoData’
getSIFromND: no visible global function definition for ‘Rle’
ks_test: no visible global function definition for ‘ks.test’
newSeqReads: no visible global function definition for ‘read.table’
newSeqReadsFromGene: no visible global function definition for
  ‘gene.details’
parseGff3: no visible global function definition for ‘read.table’
parseGff3: no visible global function definition for ‘write.table’
plotCoverageHistogram: no visible global function definition for ‘plot’
plotCoverageHistogram: no visible global function definition for
  ‘lines’
plotExonCoverage: no visible global function definition for
  ‘topo.colors’
plotExonCoverage: no visible global function definition for
  ‘exon.details’
plotExonCoverage: no visible global function definition for ‘par’
plotExonCoverage: no visible global function definition for ‘plot’
plotExonCoverage: no visible global function definition for ‘lines’
plotExonCoverage: no visible global function definition for ‘legend’
plotGeneCoverage: no visible global function definition for ‘par’
plotGeneCoverage: no visible global function definition for
  ‘topo.colors’
plotGeneCoverage: no visible global function definition for
  ‘gene.details’
plotGeneCoverage: no visible global function definition for ‘plot’
plotGeneCoverage: no visible global function definition for ‘lines’
plotGeneCoverage: no visible global function definition for ‘legend’
plotGeneExonCoverage: no visible global function definition for ‘par’
plotGeneExonCoverage: no visible global function definition for
  ‘topo.colors’
plotGeneExonCoverage: no visible global function definition for
  ‘gene.details’
plotGeneExonCoverage: no visible global function definition for
  ‘exon.details’
plotGeneExonCoverage: no visible global function definition for
  ‘gene.to.exon’
plotGeneExonCoverage: no visible global function definition for ‘plot’
plotGeneExonCoverage: no visible global function definition for ‘lines’
plotGeneExonCoverage: no visible global function definition for ‘rect’
plotGeneExonCoverage: no visible global function definition for
  ‘legend’
plotRegionCoverage: no visible global function definition for
  ‘topo.colors’
plotRegionCoverage: no visible global function definition for ‘par’
plotRegionCoverage: no visible global function definition for ‘plot’
plotRegionCoverage: no visible global function definition for ‘lines’
plotSI: no visible global function definition for ‘plot’
plotSI: no visible global function definition for ‘lines’
plotSI: no visible global function definition for ‘legend’
qq_derivative_plot: no visible global function definition for ‘qqplot’
qq_plot: no visible global function definition for ‘qqplot’
setSpecies: no visible global function definition for ‘menu’
simplePlot: no visible global function definition for ‘plot’
simplePlot: no visible global function definition for ‘lines’
spaceInChromosome: no visible binding for global variable ‘out’
sumND: no visible global function definition for ‘Rle’
Undefined global functions or variables:
  Rle dbGetQuery exon.details gene.details gene.to.exon
  gene.to.transcript ks.test legend lines menu out par phenoData
  phenoData<- plot qqplot read.table rect topo.colors
  transcript.to.exon write.table
Consider adding
  importFrom("grDevices", "topo.colors")
  importFrom("graphics", "legend", "lines", "par", "plot", "rect")
  importFrom("stats", "ks.test", "qqplot")
  importFrom("utils", "menu", "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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/rnaSeqMap.Rcheck/00check.log’
for details.

* installing *source* package ‘rnaSeqMap’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rinit.c -o Rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gcoverage.c -o gcoverage.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ghistogram.c -o ghistogram.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c regionmining.c -o regionmining.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c splicingind.c -o splicingind.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rnaSeqMap.so Rinit.o gcoverage.o ghistogram.o regionmining.o splicingind.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/rnaSeqMap.Rcheck/rnaSeqMap/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rnaSeqMap)

name	user	system	elapsed
addBamData	0.000	0.000	0.001
addDataToReadset	0.001	0.000	0.001
addExperimentsToReadset	0.001	0.000	0.001
averageND	0.000	0.000	0.001
bam2sig	0.001	0.000	0.001
buildDESeq	0.000	0.000	0.001
buildDGEList	0.000	0.000	0.001
findRegionsAsIR	0.000	0.000	0.001
findRegionsAsND	0.000	0.000	0.001
gRanges2CamelMeasures	0	0	0
geneInChromosome	0.001	0.001	0.000
generators	0.002	0.000	0.001
getBamData	0.001	0.000	0.001
getCoverageFromRS	0.001	0.000	0.000
getFCFromND	0.001	0.000	0.001
getSIFromND	0.001	0.000	0.001
getSumsExp	0.001	0.000	0.001
measures	0.000	0.000	0.001
normalizations	0.000	0.000	0.001
normalizeBySum	0.001	0.000	0.001
parseGff3	0.001	0.001	0.001
plotGeneCoverage	0.001	0.000	0.001
readsInRange	0.001	0.000	0.001
regionBasedCoverage	0.001	0.000	0.001
regionCoverage	0.001	0.000	0.000
rs.list	0.001	0.000	0.001
setSpecies	0.001	0.000	0.001
spaceInChromosome	0.001	0.000	0.000