recoup 0.99.4
Panagiotis Moulos
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/recoup | | Last Changed Rev: 115681 / Revision: 116626 | | Last Changed Date: 2016-04-02 09:31:03 -0700 (Sat, 02 Apr 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / 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_0.99.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/recoup.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘0.99.4’
* 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 ... [14s/14s] 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
areColors : <anonymous>: no visible global function definition for
‘col2rgb’
buildAnnotationStore: no visible global function definition for
‘Seqinfo’
calcDesignPlotProfiles : <anonymous>: no visible global function
definition for ‘smooth.spline’
calcPlotProfiles : <anonymous>: no visible global function definition
for ‘smooth.spline’
cmclapply: no visible global function definition for ‘mclapply’
coverageFromBam: no visible global function definition for
‘ScanBamParam’
coverageFromBam: no visible global function definition for ‘quantile’
coverageFromBam: no visible global function definition for
‘seqlevels<-’
coverageFromRanges: no visible global function definition for
‘subjectHits’
getGcContent: no visible global function definition for
‘packageVersion’
getGcContent: no visible global function definition for ‘Rle’
getGcContent: no visible global function definition for ‘IRanges’
getGcContent: no visible global function definition for
‘alphabetFrequency’
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 ‘download.file’
getUcscDbl: no visible global function definition for ‘unzip’
getUcscDbl: no visible global function definition for ‘read.delim’
getUcscDbl: no visible global function definition for ‘dbWriteTable’
getUcscDbl: no visible global function definition for ‘dbDisconnect’
graphicsClose: no visible global function definition for ‘dev.off’
graphicsOpen: no visible global function definition for ‘dev.new’
graphicsOpen: no visible global function definition for ‘pdf’
graphicsOpen: no visible global function definition for ‘postscript’
graphicsOpen: no visible global function definition for ‘png’
graphicsOpen: no visible global function definition for ‘jpeg’
graphicsOpen: no visible global function definition for ‘bmp’
graphicsOpen: no visible global function definition for ‘tiff’
kmeansDesign: no visible global function definition for ‘kmeans’
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’
readBam: no visible global function definition for ‘quantile’
readBed: no visible global function definition for ‘seqlevels’
readBed: no visible global function definition for ‘Seqinfo’
readConfig: no visible global function definition for ‘read.delim’
recoup: no visible global function definition for ‘read.delim’
recoup: no visible binding for global variable ‘gene’
recoup: no visible binding for global variable ‘sexon’
recoup : <anonymous>: no visible global function definition for
‘runValue’
recoup : <anonymous>: no visible global function definition for
‘BigWigFile’
recoup: no visible binding for global variable ‘forcedBinSize’
recoupCorrelation : <anonymous>: no visible global function definition
for ‘lowess’
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 : <anonymous>: no visible global function definition
for ‘smooth.spline’
recoupCorrelation: no visible binding for global variable ‘Design’
recoupHeatmap : <anonymous>: no visible global function definition for
‘grid.text’
recoupHeatmap: no visible global function definition for ‘quantile’
recoupHeatmap : <anonymous>: no visible global function definition for
‘quantile’
recoupPlot: no visible global function definition for ‘dev.new’
recoupPlot: no visible global function definition for ‘plot’
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’
setr: no visible global function definition for ‘read.delim’
splitVector: no visible global function definition for ‘spline’
splitVector: no visible global function definition for ‘approx’
splitVector: no visible global function definition for ‘Rle’
ssCI: no visible global function definition for ‘var’
Undefined global functions or variables:
BigWigFile Condition Coverage DataFrame Design IRanges Index Rle
ScanBamParam Seqinfo Signal alphabetFrequency approx biocLite bmp
col2rgb dbConnect dbDisconnect dbDriver dbGetQuery dbWriteTable
dev.new dev.off download.file forcedBinSize gene getBSgenome
grid.text installed.genomes jpeg kmeans lowess mclapply
packageVersion pdf plot png postscript quantile read.delim runValue
seqlevels seqlevels<- sexon smooth.spline spline subjectHits tiff
unzip var
Consider adding
importFrom("grDevices", "bmp", "col2rgb", "dev.new", "dev.off", "jpeg",
"pdf", "png", "postscript", "tiff")
importFrom("graphics", "plot")
importFrom("stats", "approx", "kmeans", "lowess", "quantile",
"smooth.spline", "spline", "var")
importFrom("utils", "download.file", "packageVersion", "read.delim",
"unzip")
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 ... [273s/95s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
coverageRnaRef 45.642 10.524 12.800
profileMatrix 19.804 6.681 6.389
recoupPlot 17.706 3.725 8.366
recoup 17.797 3.589 8.352
kmeansDesign 17.016 3.347 8.173
coverageRef 16.518 3.775 4.459
simpleGetSet 16.162 3.688 6.129
sliceObj 16.089 3.548 6.135
recoupHeatmap 14.377 2.606 6.044
recoupCorrelation 14.126 2.450 5.772
recoupProfile 13.655 2.429 5.146
calcCoverage 7.579 1.437 3.744
getAnnotation 1.165 0.099 6.453
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [87s/38s]
[87s/38s] 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-3.3-bioc/meat/recoup.Rcheck/00check.log’
for details.