flowStats 3.26.1
Greg Finak and Mike Jiang
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/flowStats | | Last Changed Rev: 109384 / Revision: 109384 | | Last Changed Date: 2015-10-08 14:52:23 -0700 (Thu, 08 Oct 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | ERROR | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | ERROR | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | ERROR | OK | |
| morelia | 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 flowStats_3.26.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/flowStats.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowStats’ version ‘3.26.1’
* 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 ‘flowStats’ can be installed ... [12s/13s] 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’ ‘fda’
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
Package in Depends field not imported from: ‘cluster’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Missing or unexported object: ‘flowWorkspace::getDimensions’
Missing object imported by a ':::' call: ‘flowWorkspace:::.isBooleanGate.graphNEL’
Unexported objects imported by ':::' calls:
‘flowCore:::checkClass’ ‘flowCore:::copyFlowSet’
‘flowCore:::findTimeChannel’ ‘flowCore:::inpolygon’
‘flowViz:::plotType’ ‘flowWorkspace:::.isBoolGate’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘backGating’ ‘curvPeaks’ ‘getPeakRegions’ ‘idFeaturesByBackgating’
‘landmarkMatrixWithoutFilterResult’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
%in%,flowFrame-lymphFilter: warning in lymphGate(x, channels =
parameters(table), preselection = pre, scale = table@scale, bwFac =
table@bwFac, filterId = table@filterId, eval = TRUE, plot = FALSE):
partial argument match of 'eval' to 'evaluate'
.normalizeGatingSet: no visible global function definition for
‘getNodes’
.normalizeGatingSet: no visible global function definition for ‘clone’
.normalizeGatingSet: no visible global function definition for
‘getGate’
.normalizeGatingSet: no visible global function definition for
‘getParent’
.normalizeGatingSet: no visible global function definition for
‘flowData<-’
.normalizeGatingSet: no visible global function definition for
‘flowData’
.normalizeGatingSet: no visible global function definition for
‘recompute’
.plotGPAprocess: no visible binding for global variable ‘whichS’
.plotGPAprocess: no visible binding for global variable ‘cluster’
.plotWorkFlow: no visible binding for global variable ‘cluster’
.plotWorkFlow: no visible binding for global variable ‘bogus’
.usingSVD: no visible binding for global variable ‘params’
density1d_simple: no visible binding for global variable ‘y’
fdPar: no visible global function definition for ‘fd’
fdPar: no visible global function definition for ‘vec2Lfd’
fdPar: no visible global function definition for ‘norder.bspline’
fdPar: no visible global function definition for ‘int2Lfd’
normQA: no visible binding for global variable ‘group’
normQA: no visible binding for global variable ‘hasPeak’
singletGate: no visible global function definition for ‘polygonGate’
warpSetNCDF: no visible global function definition for
‘clone.ncdfFlowSet’
addName,curv1Filter-character : .local: no visible global function
definition for ‘identifier’
addName,curv1Filter-character : .local: no visible global function
definition for ‘checkParameterMatch’
addName,curv1Filter-character : .local: no visible global function
definition for ‘addName’
addName,curv1Filter-logical : .local: no visible global function
definition for ‘addName’
addName,curv2Filter-character : .local: no visible global function
definition for ‘identifier’
addName,curv2Filter-character : .local: no visible global function
definition for ‘checkParameterMatch’
addName,curv2Filter-character : .local: no visible global function
definition for ‘addName’
addName,curv2Filter-character : .local: no visible global function
definition for ‘polygonGate’
addName,curv2Filter-logical : .local: no visible global function
definition for ‘addName’
densityplot,view-missing : .local: no visible global function
definition for ‘Data’
glines,curv1Filter-ANY : .local: no visible global function definition
for ‘evalError’
glines,curv1Filter-flowFrame : .local: no visible global function
definition for ‘glines’
glines,curv1Filter-missing : .local: no visible global function
definition for ‘evalError’
glines,curv1Filter-multipleFilterResult : .local: no visible global
function definition for ‘identifier’
glines,curv1Filter-multipleFilterResult : .local: no visible global
function definition for ‘brewer.pal’
glines,curv1Filter-multipleFilterResult : .local : <anonymous>: no
visible global function definition for ‘glines’
glines,curv2Filter-ANY : .local: no visible global function definition
for ‘evalError’
glines,curv2Filter-flowFrame : .local: no visible global function
definition for ‘glines’
glines,curv2Filter-multipleFilterResult : .local: no visible global
function definition for ‘identifier’
glines,curv2Filter-multipleFilterResult : .local: no visible global
function definition for ‘brewer.pal’
glines,curv2Filter-multipleFilterResult : .local : <anonymous>: no
visible global function definition for ‘glines’
glines,curv2Filter-multipleFilterResult : .local : <anonymous>: no
visible global function definition for ‘polygonGate’
glpoints,curv1Filter-flowFrame-character : .local: no visible global
function definition for ‘flowViz.par.get’
glpoints,curv1Filter-flowFrame-character : .local: no visible global
function definition for ‘multFiltPoints’
glpoints,curv1Filter-flowFrame-character : .local: no visible global
function definition for ‘addName’
glpoints,curv2Filter-flowFrame-character : .local: no visible global
function definition for ‘flowViz.par.get’
glpoints,curv2Filter-flowFrame-character : .local: no visible global
function definition for ‘multFiltPoints’
glpoints,curv2Filter-flowFrame-character : .local: no visible global
function definition for ‘addName’
glpolygon,curv1Filter-ANY: no visible global function definition for
‘evalError’
glpolygon,curv1Filter-flowFrame : .local: no visible global function
definition for ‘flowViz.par.get’
glpolygon,curv1Filter-multipleFilterResult : .local: no visible global
function definition for ‘flowViz.par.get’
glpolygon,curv1Filter-multipleFilterResult : .local: no visible global
function definition for ‘identifier’
glpolygon,curv2Filter-ANY: no visible global function definition for
‘evalError’
glpolygon,curv2Filter-flowFrame : .local: no visible global function
definition for ‘flowViz.par.get’
glpolygon,curv2Filter-multipleFilterResult : .local: no visible global
function definition for ‘flowViz.par.get’
glpolygon,curv2Filter-multipleFilterResult : .local: no visible global
function definition for ‘identifier’
glpolygon,curv2Filter-multipleFilterResult : .local: no visible global
function definition for ‘polygonGate’
gpoints,curv1Filter-flowFrame-character : .local: no visible global
function definition for ‘checkParameterMatch’
gpoints,curv1Filter-flowFrame-character : .local: no visible global
function definition for ‘identifier’
gpoints,curv1Filter-flowFrame-character : .local: no visible global
function definition for ‘brewer.pal’
gpoints,curv2Filter-flowFrame-character : .local: no visible global
function definition for ‘checkParameterMatch’
gpoints,curv2Filter-flowFrame-character : .local: no visible global
function definition for ‘identifier’
gpoints,curv2Filter-flowFrame-character : .local: no visible global
function definition for ‘brewer.pal’
gpolygon,curv1Filter-ANY : .local: no visible global function
definition for ‘evalError’
gpolygon,curv1Filter-flowFrame : .local: no visible global function
definition for ‘gpolygon’
gpolygon,curv1Filter-missing : .local: no visible global function
definition for ‘evalError’
gpolygon,curv1Filter-multipleFilterResult : .local: no visible global
function definition for ‘identifier’
gpolygon,curv1Filter-multipleFilterResult : .local: no visible global
function definition for ‘brewer.pal’
gpolygon,curv1Filter-multipleFilterResult : .local : <anonymous>: no
visible global function definition for ‘gpolygon’
gpolygon,curv2Filter-ANY : .local: no visible global function
definition for ‘evalError’
gpolygon,curv2Filter-flowFrame : .local: no visible global function
definition for ‘gpolygon’
gpolygon,curv2Filter-multipleFilterResult : .local: no visible global
function definition for ‘identifier’
gpolygon,curv2Filter-multipleFilterResult : .local: no visible global
function definition for ‘brewer.pal’
gpolygon,curv2Filter-multipleFilterResult : .local : <anonymous>: no
visible global function definition for ‘gpolygon’
gpolygon,curv2Filter-multipleFilterResult : .local : <anonymous>: no
visible global function definition for ‘polygonGate’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘flowStats-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lymphFilter-class
> ### Title: Automated gating of elliptical cell populations in 2D.
> ### Aliases: lymphFilter-class %in%,flowFrame,lymphFilter-method lymphGate
> ### lymphFilter
> ### Keywords: misc classes
>
> ### ** Examples
>
>
> data(GvHD)
> dat <- GvHD[pData(GvHD)$Patient==10]
> dat <- transform(dat, "FL4-H"=asinh(`FL4-H`))
> lg <- lymphGate(dat, channels=c("FSC-H", "SSC-H"), preselection="FL4-H",scale=1.5)
>
> if(require(flowViz))
+ xyplot(`SSC-H`˜`FSC-H`, dat, filter=lg$n2gate)
>
> ## This is using the abstract lymphFilter class instead
> lf <- lymphFilter(channels=c("FSC-H", "SSC-H"), preselection="FL4-H")
Error: 'lymphFilter' is defunct.
See help("Defunct")
Execution halted
* 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 ERROR, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/flowStats.Rcheck/00check.log’
for details.