rnaSeqMap 2.32.0
Michal Okoniewski
| 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/rnaSeqMap | | 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 | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
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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_2.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/rnaSeqMap.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 ‘rnaSeqMap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rnaSeqMap’ version ‘2.32.0’
* 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-3.4-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 -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Rinit.c -o Rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c gcoverage.c -o gcoverage.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c ghistogram.c -o ghistogram.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c regionmining.c -o regionmining.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -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-3.4-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)