CRImage 1.22.0
Henrik Failmezger , Yinyin Yuan
| 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/CRImage | | Last Changed Rev: 123155 / Revision: 128728 | | Last Changed Date: 2016-10-28 13:53:44 -0400 (Fri, 28 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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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CRImage_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/CRImage.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CRImage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CRImage’ version ‘1.22.0’
* 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 ‘CRImage’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.9Mb
sub-directories of 1Mb or more:
doc 1.4Mb
extdata 5.4Mb
* 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
‘DNAcopy’ ‘aCGH’
Please remove these calls from your code.
':::' call which should be '::': ‘aCGH:::combine.func’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Phansalkar_threshold: no visible global function definition for ‘sd’
SauvolaThreshold: no visible global function definition for ‘sd’
calculateMeanStdTarget: no visible global function definition for ‘sd’
calculateOtsu: no visible global function definition for ‘optimize’
classificationAperio: no visible global function definition for
‘write.table’
classificationAperio: no visible global function definition for
‘read.table’
classifyCells: no visible global function definition for ‘predict’
classifyPen: no visible global function definition for ‘predict’
colorCorrection: no visible global function definition for ‘sd’
correctCopyNumber : Myansari.test.default: no visible global function
definition for ‘complete.cases’
correctCopyNumber : Myansari.test.default: no visible global function
definition for ‘pnorm’
correctCopyNumber : Myansari.test.default : ccia: no visible global
function definition for ‘qnorm’
correctCopyNumber : Myansari.test.default : ccia: no visible global
function definition for ‘uniroot’
correctCopyNumber : Myansari.test.default: no visible global function
definition for ‘uniroot’
correctCopyNumber: no visible global function definition for ‘quantile’
correctCopyNumber: no visible global function definition for ‘median’
determineCellularity: no visible global function definition for
‘colorRampPalette’
determineCellularity: no visible global function definition for
‘col2rgb’
findSlices: no visible global function definition for ‘cutree’
findSlices: no visible global function definition for ‘hclust’
findSlices: no visible global function definition for ‘dist’
findSlices: no visible global function definition for ‘col2rgb’
kernelSmoother: no visible global function definition for ‘dist’
labelCells: no visible global function definition for ‘points’
labelCells: no visible global function definition for ‘title’
labelCells : refresh: no visible global function definition for
‘points’
labelCells : refresh: no visible global function definition for ‘title’
labelCells : refresh: no visible global function definition for
‘write.table’
labelCells : keydown: no visible global function definition for
‘write.table’
labelCells : keydown: no visible global function definition for ‘title’
labelCells : dragmousedown: no visible global function definition for
‘grconvertX’
labelCells : dragmousedown: no visible global function definition for
‘grconvertY’
labelCells : dragmousemove: no visible global function definition for
‘grconvertX’
labelCells : dragmousemove: no visible global function definition for
‘grconvertY’
labelCells : dragmousemove: no visible global function definition for
‘lines’
labelCells : dragmouseup: no visible global function definition for
‘chull’
labelCells : dragmouseup: no visible global function definition for
‘grconvertX’
labelCells : dragmouseup: no visible global function definition for
‘grconvertY’
labelCells: no visible global function definition for
‘setGraphicsEventHandlers’
labelCells: no visible global function definition for
‘getGraphicsEvent’
numberOfNeighbors: no visible global function definition for ‘dist’
plotCorrectedCN: no visible global function definition for ‘par’
plotCorrectedCN: no visible global function definition for ‘plot’
plotCorrectedCN: no visible global function definition for ‘segments’
plotCorrectedCN: no visible global function definition for ‘title’
plotImage: no visible global function definition for ‘grey’
plotImage: no visible global function definition for ‘rgb’
processAperio: no visible global function definition for ‘write.table’
processAperio: no visible global function definition for ‘col2rgb’
segmentStructures: no visible global function definition for ‘predict’
Undefined global functions or variables:
chull col2rgb colorRampPalette complete.cases cutree dist
getGraphicsEvent grconvertX grconvertY grey hclust lines median
optimize par plot pnorm points predict qnorm quantile read.table rgb
sd segments setGraphicsEventHandlers title uniroot write.table
Consider adding
importFrom("grDevices", "chull", "col2rgb", "colorRampPalette",
"getGraphicsEvent", "grey", "rgb",
"setGraphicsEventHandlers")
importFrom("graphics", "grconvertX", "grconvertY", "lines", "par",
"plot", "points", "segments", "title")
importFrom("stats", "complete.cases", "cutree", "dist", "hclust",
"median", "optimize", "pnorm", "predict", "qnorm",
"quantile", "sd", "uniroot")
importFrom("utils", "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 sizes of PDF files under ‘inst/doc’ ... 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
calculateCellularity 5.170 1.069 6.333
classifyCells 4.025 1.063 5.187
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.4-bioc/meat/CRImage.Rcheck/00check.log’
for details.