recoup 1.1.2
Panagiotis Moulos
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/recoup | | Last Changed Rev: 117512 / Revision: 121152 | | Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (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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### rm -rf recoup.buildbin-libdir recoup.Rcheck && mkdir recoup.buildbin-libdir recoup.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=recoup.buildbin-libdir recoup_1.1.2.tar.gz >recoup.Rcheck\00install.out 2>&1 && cp recoup.Rcheck\00install.out recoup-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=recoup.buildbin-libdir --install="check:recoup-install.out" --force-multiarch --no-vignettes --timings recoup_1.1.2.tar.gz
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/recoup.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'recoup/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'recoup' version '1.1.2'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
coverageRnaRef 28.50 0.33 28.83
recoupPlot 14.33 0.13 14.47
recoup 14.01 0.12 14.54
kmeansDesign 13.12 0.09 13.22
sliceObj 12.51 0.01 12.52
simpleGetSet 12.24 0.05 12.30
profileMatrix 11.38 0.05 11.43
recoupProfile 10.28 0.01 10.29
recoupHeatmap 10.27 0.00 10.26
recoupCorrelation 10.23 0.00 10.23
calcCoverage 9.96 0.24 10.20
coverageRef 9.72 0.06 9.78
getAnnotation 1.22 0.03 7.63
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
coverageRnaRef 34.32 0.38 34.71
recoupPlot 16.68 0.09 16.77
recoup 16.05 0.08 16.22
kmeansDesign 14.57 0.10 14.69
simpleGetSet 14.12 0.02 14.13
sliceObj 14.09 0.04 14.14
profileMatrix 13.10 0.05 13.15
recoupProfile 12.59 0.00 12.59
recoupCorrelation 12.14 0.03 12.17
recoupHeatmap 12.06 0.00 12.07
coverageRef 11.93 0.03 11.97
calcCoverage 8.21 0.05 8.25
getAnnotation 1.03 0.01 6.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'D:/biocbld/bbs-3.4-bioc/meat/recoup.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'recoup' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'recoup' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'recoup' as recoup_1.1.2.zip
* DONE (recoup)