flowDensity 1.6.0
Mehrnoush Malek
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/flowDensity | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings flowDensity_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/flowDensity.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowDensity/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowDensity’ version ‘1.6.0’
* 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 ‘flowDensity’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
doc 1.0Mb
extdata 4.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’
A package should be listed in only one of these fields.
* 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
Namespace in Imports field not imported from: ‘graphics’
All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘.densityGating’ ‘.ellipseGating’ ‘nmRemove’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.deGate2D: no visible global function definition for ‘chull’
.deGatePlot: no visible global function definition for ‘par’
.deGatePlot: no visible global function definition for ‘polygon’
.deGatePlot: no visible global function definition for ‘abline’
.deGatePlot: no visible global function definition for ‘colors’
.deGatePlot: no visible global function definition for ‘mtext’
.densityForPlot: no visible global function definition for ‘density’
.densityForPlot: no visible global function definition for
‘smooth.spline’
.densityGating: no visible global function definition for ‘sd’
.densityGating: no visible global function definition for ‘median’
.densityGating: no visible global function definition for ‘quantile’
.densityGating: no visible global function definition for ‘abline’
.flowDensity.2d: no visible global function definition for ‘chull’
.getIntersect: no visible global function definition for ‘splinefun’
.getScoreIndex: no visible global function definition for ‘splinefun’
.layoutCreate: no visible global function definition for ‘layout’
.layoutCreate: no visible global function definition for ‘layout.show’
.notSubFrame: no visible global function definition for ‘chull’
plotDens: no visible global function definition for ‘densCols’
plotDens: no visible global function definition for ‘png’
plotDens: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
abline chull colors densCols density dev.off layout layout.show
median mtext par png polygon quantile sd smooth.spline splinefun
Consider adding
importFrom("grDevices", "chull", "colors", "densCols", "dev.off",
"png")
importFrom("graphics", "abline", "layout", "layout.show", "mtext",
"par", "polygon")
importFrom("stats", "density", "median", "quantile", "sd",
"smooth.spline", "splinefun")
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 ... WARNING
Codoc mismatches from documentation object 'deGate':
deGate
Code: function(flow.frame, channel, n.sd = 1.5, use.percentile =
FALSE, percentile = 0.95, upper = NA, alpha = 0.1,
sd.threshold = FALSE, graphs = FALSE, all.cut = FALSE,
tinypeak.removal = 1/25, adjust.dens = 1)
Docs: function(flow.frame, channel, n.sd = 1.5, use.percentile =
FALSE, percentile = 0.95, upper = NA, alpha = 0.1,
sd.threshold = FALSE, graphs = FALSE, all.cut = FALSE,
tinypeak.removal = 1/25)
Argument names in code not in docs:
adjust.dens
Codoc mismatches from documentation object 'nmRemove':
nmRemove
Code: function(flow.frame, channels, neg = F, talk = FALSE)
Docs: function(flow.frame, channels, neg = TRUE, talk = FALSE)
Mismatches in argument default values:
Name: 'neg' Code: F Docs: TRUE
Codoc mismatches from documentation object 'plotDens':
plotDens
Code: function(flow.frame, channels, col, main, xlab, ylab, pch =
".", s = FALSE, outdir, file.name, ...)
Docs: function(flow.frame, channels, col, main, xlab, ylab, pch =
".", s = FALSE, outdir, file.name, devn = TRUE, ...)
Argument names in docs not in code:
devn
Mismatches in argument names:
Position: 11 Code: ... Docs: devn
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'deGate':
‘adjust.dens’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
* 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: 2 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/flowDensity.Rcheck/00check.log’
for details.