Michal Okoniewski
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/rnaSeqMap |
| Branch: RELEASE_3_9 |
| Last Commit: 3a3a103 |
| Last Changed Date: 2019-05-02 11:53:19 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:48:24 -0400 (Wed, 16 Oct 2019).
| Package 1398/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rnaSeqMap 2.42.0 Michal Okoniewski
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: rnaSeqMap |
| Version: 2.42.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rnaSeqMap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rnaSeqMap_2.42.0.tar.gz |
| StartedAt: 2019-10-16 06:21:06 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:26:20 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 314.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rnaSeqMap.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rnaSeqMap.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rnaSeqMap_2.42.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/rnaSeqMap.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.42.0’
* 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/rnaSeqMap.Rcheck/00check.log’
for details.
rnaSeqMap.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rnaSeqMap ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘rnaSeqMap’ ... ** using staged installation ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Rinit.c -o Rinit.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c gcoverage.c -o gcoverage.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ghistogram.c -o ghistogram.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c regionmining.c -o regionmining.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-rnaSeqMap/00new/rnaSeqMap/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rnaSeqMap)
rnaSeqMap.Rcheck/rnaSeqMap-Ex.timings
| name | user | system | elapsed | |
| addBamData | 0.001 | 0.000 | 0.000 | |
| addDataToReadset | 0.001 | 0.001 | 0.001 | |
| addExperimentsToReadset | 0.000 | 0.000 | 0.001 | |
| averageND | 0 | 0 | 0 | |
| bam2sig | 0.001 | 0.000 | 0.001 | |
| buildDESeq | 0.000 | 0.000 | 0.001 | |
| buildDGEList | 0.000 | 0.000 | 0.001 | |
| findRegionsAsIR | 0 | 0 | 0 | |
| findRegionsAsND | 0 | 0 | 0 | |
| gRanges2CamelMeasures | 0.001 | 0.000 | 0.000 | |
| geneInChromosome | 0.000 | 0.000 | 0.001 | |
| generators | 0.001 | 0.000 | 0.001 | |
| getBamData | 0 | 0 | 0 | |
| getCoverageFromRS | 0.001 | 0.001 | 0.001 | |
| getFCFromND | 0.000 | 0.001 | 0.001 | |
| getSIFromND | 0.000 | 0.001 | 0.001 | |
| getSumsExp | 0.000 | 0.001 | 0.000 | |
| measures | 0.000 | 0.000 | 0.001 | |
| normalizations | 0.001 | 0.000 | 0.001 | |
| normalizeBySum | 0.000 | 0.001 | 0.000 | |
| parseGff3 | 0.001 | 0.000 | 0.000 | |
| plotGeneCoverage | 0.000 | 0.000 | 0.001 | |
| readsInRange | 0 | 0 | 0 | |
| regionBasedCoverage | 0.001 | 0.001 | 0.001 | |
| regionCoverage | 0.001 | 0.000 | 0.000 | |
| rs.list | 0.000 | 0.000 | 0.001 | |
| setSpecies | 0 | 0 | 0 | |
| spaceInChromosome | 0.000 | 0.000 | 0.001 | |