recoup 1.2.0
Panagiotis Moulos
| 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/recoup | | 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 | NotNeeded | OK | [ OK ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / 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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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings recoup_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/recoup.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.0’
* 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
areColors : <anonymous>: no visible global function definition for
‘col2rgb’
buildAnnotationStore: no visible global function definition for
‘Seqinfo’
calcCoverage: no visible global function definition for ‘is’
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 ‘is’
coverageFromBam: no visible global function definition for
‘ScanBamParam’
coverageFromBam: no visible global function definition for ‘as’
coverageFromBam: no visible global function definition for ‘quantile’
coverageFromBam: no visible global function definition for
‘seqlevels<-’
coverageFromBigWig: no visible global function definition for ‘is’
coverageFromRanges: no visible global function definition for ‘is’
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 ‘as’
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 ‘is’
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 as biocLite bmp
col2rgb dbConnect dbDisconnect dbDriver dbGetQuery dbWriteTable
dev.new dev.off download.file forcedBinSize gene getBSgenome
grid.text installed.genomes is 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("methods", "as", "is")
importFrom("stats", "approx", "kmeans", "lowess", "quantile",
"smooth.spline", "spline", "var")
importFrom("utils", "download.file", "packageVersion", "read.delim",
"unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
coverageRnaRef 47.832 12.692 9.223
simpleGetSet 17.560 7.900 6.334
recoup 19.184 6.088 7.333
recoupPlot 18.552 6.620 7.871
profileMatrix 17.644 6.880 4.542
sliceObj 16.980 7.476 6.173
kmeansDesign 18.140 5.508 6.986
coverageRef 18.104 3.740 3.376
recoupProfile 15.136 4.712 4.373
recoupCorrelation 15.396 4.048 4.161
recoupHeatmap 14.988 3.708 4.174
calcCoverage 10.124 1.888 3.102
getAnnotation 1.448 0.060 5.495
* 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
‘/home/biocbuild/bbs-3.4-bioc/meat/recoup.Rcheck/00check.log’
for details.