recoup 1.4.0
Panagiotis Moulos
| 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/recoup | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | 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 recoup_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/recoup.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recoup/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘recoup’ version ‘1.4.0’
* package encoding: UTF-8
* 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 ‘recoup’ 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 loading without being on the library search path ... 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
baseCoverageMatrix: no visible global function definition for
‘runValue’
baseCoverageMatrix : <anonymous>: no visible global function definition
for ‘runValue’
binCoverageMatrix : <anonymous>: no visible global function definition
for ‘runValue’
buildAnnotationStore: no visible global function definition for
‘Seqinfo’
calcCoverage: no visible global function definition for ‘runValue’
cleanRanges: no visible global function definition for ‘seqlevels’
cleanRanges: no visible global function definition for ‘seqlevels<-’
cmclapply: no visible global function definition for ‘mclapply’
cmcmapply: no visible global function definition for ‘mcmapply’
coverageFromBam: no visible global function definition for
‘ScanBamParam’
coverageFromBam: no visible global function definition for
‘seqlevels<-’
coverageFromBigWig : <anonymous> : <anonymous>: no visible global
function definition for ‘Rle’
coverageFromBigWig: no visible global function definition for ‘Rle’
coverageFromBigWig : <anonymous>: no visible global function definition
for ‘Rle’
coverageFromRanges: no visible global function definition for
‘subjectHits’
coverageFromRanges : <anonymous> : <anonymous>: no visible global
function definition for ‘Rle’
coverageFromRanges: no visible global function definition for ‘Rle’
coverageFromRangesOld: no visible global function definition for
‘subjectHits’
getGcContent: no visible global function definition for ‘Rle’
getGcContent: no visible global function definition for ‘IRanges’
getGcContent: no visible global function definition for
‘alphabetFrequency’
getMainRnaRangesOnTheFly: no visible binding for global variable
‘genomeRanges’
getUcscAnnotation: no visible global function definition for ‘dbDriver’
getUcscAnnotation: no visible global function definition for
‘dbConnect’
getUcscAnnotation: no visible global function definition for
‘dbGetQuery’
getUcscAnnotation: no visible global function definition for
‘dbDisconnect’
getUcscDbl: no visible global function definition for ‘dbDriver’
getUcscDbl: no visible global function definition for ‘dbConnect’
getUcscDbl: no visible global function definition for ‘dbWriteTable’
getUcscDbl: no visible global function definition for ‘dbDisconnect’
loadBsGenome: no visible global function definition for
‘installed.genomes’
loadBsGenome: no visible global function definition for ‘getBSgenome’
loadBsGenome: no visible global function definition for ‘biocLite’
prepareBam: no visible global function definition for ‘indexBam’
prepareBam : <anonymous>: no visible global function definition for
‘sortBam’
prepareBam : <anonymous>: no visible global function definition for
‘indexBam’
preprocessRanges: no visible global function definition for
‘ScanBamParam’
preprocessRanges: no visible global function definition for
‘bamWhich<-’
readBed: no visible global function definition for ‘seqlevels’
readBed: no visible global function definition for ‘Seqinfo’
recoup: no visible binding for global variable ‘gene’
recoup: no visible binding for global variable ‘sexon’
recoup: no visible binding for global variable ‘flankedSexon’
recoup : <anonymous>: no visible global function definition for
‘runValue’
recoupCorrelation: no visible binding for global variable ‘Index’
recoupCorrelation: no visible binding for global variable ‘Coverage’
recoupCorrelation: no visible binding for global variable ‘Condition’
recoupCorrelation: no visible binding for global variable ‘Design’
recoupHeatmap : <anonymous>: no visible global function definition for
‘grid.text’
recoupProfile: no visible binding for global variable ‘Signal’
recoupProfile: no visible binding for global variable ‘Condition’
recoupProfile: no visible binding for global variable ‘Design’
reduceExons : <anonymous>: no visible global function definition for
‘DataFrame’
splitVector: no visible global function definition for ‘Rle’
Undefined global functions or variables:
Condition Coverage DataFrame Design IRanges Index Rle ScanBamParam
Seqinfo Signal alphabetFrequency bamWhich<- biocLite dbConnect
dbDisconnect dbDriver dbGetQuery dbWriteTable flankedSexon gene
genomeRanges getBSgenome grid.text indexBam installed.genomes
mclapply mcmapply runValue seqlevels seqlevels<- sexon sortBam
subjectHits
* 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
Examples with CPU or elapsed time > 5s
user system elapsed
profileMatrix 20.528 9.423 14.787
mergeRuns 17.605 4.396 15.928
kmeansDesign 6.869 2.104 6.252
recoup 6.221 2.148 5.206
recoupPlot 6.098 2.270 5.189
simpleGetSet 4.752 2.268 3.461
sliceObj 4.714 2.141 3.699
coverageRef 4.573 0.420 5.126
getAnnotation 0.977 0.038 5.283
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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-3.5-bioc/meat/recoup.Rcheck/00check.log’
for details.