flowViz 1.39.1
Mike Jiang
| Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowViz | | Last Changed Rev: 125453 / Revision: 127142 | | Last Changed Date: 2016-12-27 14:15:45 -0500 (Tue, 27 Dec 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | ERROR | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | ERROR | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ ERROR ] | 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 flowViz_1.39.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowViz.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowViz’ version ‘1.39.1’
* 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 ‘flowViz’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘flowCore’ ‘lattice’
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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘flowCore:::findTimeChannel’ ‘flowCore:::prepareSet’
‘lattice:::hist.constructor’ ‘lattice:::updateList’
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
flowPlot,flowFrame: warning in log(xd, b = 10): partial argument match
of 'b' to 'base'
flowPlot,flowFrame: warning in log(yd, b = 10): partial argument match
of 'b' to 'base'
.process_overlay_flowSet : <anonymous>: no visible global function
definition for ‘extends’
.xyplot.flowSet: no visible global function definition for ‘as.formula’
panel.densityplot.flowset.stack: no visible binding for global variable
‘rl’
panel.xyplot.flowframe: no visible global function definition for
‘densCols’
panel.xyplot.flowframe.old: no visible global function definition for
‘densCols’
prepanel.densityplot.flowset.stack: no visible global function
definition for ‘extends’
contour,flowFrame: no visible global function definition for
‘contourLines’
flowPlot,flowFrame: no visible global function definition for ‘rainbow’
glpoints,filter-flowFrame-missing: no visible binding for global
variable ‘parms’
glpoints,filter-flowFrame-missing: no visible binding for global
variable ‘strict’
gpoints,quadGate-flowFrame-character: no visible binding for global
variable ‘filterResult’
gpolygon,ellipsoidGate-character: no visible binding for global
variable ‘fd’
Undefined global functions or variables:
as.formula contourLines densCols extends fd filterResult parms
rainbow rl strict
Consider adding
importFrom("grDevices", "contourLines", "densCols", "rainbow")
importFrom("methods", "extends")
importFrom("stats", "as.formula")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: glines-methods.Rd:149-151: Dropping empty section ‘Methods’
prepare_Rd: timeLinePlot.Rd:72-74: Dropping empty section ‘Methods’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘flowViz-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xyplot,flowFrame,missing-method
> ### Title: Methods implementing Lattice xyplots for flow data.
> ### Aliases: panel.xyplot.flowframe panel.xyplot.flowframe.time
> ### panel.xyplot.flowset prepanel.xyplot.flowframe
> ### prepanel.xyplot.flowframe.time prepanel.xyplot.flowset xyplot
> ### xyplot,flowFrame,missing-method xyplot,formula,flowFrame-method
> ### xyplot,formula,flowSet-method xyplot,formula,gateView-method
> ### xyplot,formula,view-method xyplot,view,missing-method
> ### Keywords: dplot methods
>
> ### ** Examples
>
> data(GvHD)
> GvHD <- GvHD[pData(GvHD)$Patient %in% 5:6]
>
> ## a bivariate scatterplot
> ## by default ('smooth=TRUE') panel.smoothScatter is used
> xyplot(`FSC-H` ˜ `SSC-H`, GvHD[["s5a05"]], nbin = 100,
+ main="A single flowFrame")
>
> ## A non-smooth version of the same data
> xyplot(`FSC-H` ˜ `SSC-H`, GvHD[["s5a05"]], nbin = 100,
+ main="A single flowFrame", smooth=FALSE)
>
> ## A non-smooth version of the same data with customerized color scheme
> require(IDPmisc)
Loading required package: IDPmisc
Loading required package: grid
> colramp <- colorRampPalette(IDPcolorRamp(21))
> xyplot(`FSC-H` ˜ `SSC-H`, GvHD[["s5a05"]], nbin = 100,
+ main="A single flowFrame", smooth=FALSE,
+ colramp=colramp, pch=20, cex=0.1)
>
> ## A hexbin version of non-smooth scatter plot
> xyplot(`FSC-H` ˜ `SSC-H`, GvHD[["s5a05"]], xbin = 128
+ ,main="A single flowFrame", smooth=FALSE)
>
>
> ## Visual artifacts created by the pileup of margin events
> xyplot(`FSC-H` ˜ `SSC-H`, GvHD[["s5a05"]], nbin = 100,
+ main="A single flowFrame", margin=FALSE)
>
>
> ## simple bivariate scatter plot (a.k.a. dot plot)
> ## for the whole flowSet, conditioning on Patient and
> ## Visit
> xyplot(`SSC-H` ˜ `FSC-H` | Patient:Visit, data = GvHD)
>
> ## Same bivariate scatter plot with replacing default color
> require(IDPmisc)
> cols <- colorRampPalette(IDPcolorRamp(21))
> xyplot(`SSC-H` ˜ `FSC-H` | Patient:Visit, data = GvHD, colramp=cols)
>
> ## several examples with time on the X axis
> ## first for a flowFrame
> xyplot(GvHD[[1]])
FSC-H1 FSC-H2 SSC-H1 SSC-H2 FL1-H1 FL1-H2 FL2-H1 FL2-H2 FL3-H1 FL3-H2 FL2-A1
0 1023 0 1023 1 10000 1 10000 1 10000 0
FL2-A2 FL4-H1 FL4-H2 Time1 Time2
1023 1 10000 0 1023
Error in extend.limits(limitlist[[i]], axs = axs) :
improper length of 'lim'
Calls: xyplot ... limits.and.aspect -> limitsFromLimitlist -> extend.limits
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
'::' or ':::' import not declared from: ‘data.table’
* 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 ERROR, 5 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/flowViz.Rcheck/00check.log’
for details.