flowStats 3.33.4
Greg Finak and Mike Jiang
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowStats | | Last Changed Rev: 127602 / Revision: 129046 | | Last Changed Date: 2017-03-21 19:04:18 -0400 (Tue, 21 Mar 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | 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_3.33.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowStats.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘3.33.4’
* 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 ... WARNING
Found the following significant warnings:
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/flowStats.Rcheck/00install.out’ for details.
* 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’ ‘ncdfFlow’
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
Packages in Depends field not imported from:
‘cluster’ ‘ncdfFlow’
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'
.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’
SignifFeatureRegion: no visible global function definition for ‘pchisq’
density1d_simple: no visible binding for global variable ‘y’
dfltBWrange: no visible binding for global variable ‘IQR’
fdPar: no visible global function definition for ‘norder.bspline’
gate_singlet: no visible global function definition for ‘predict’
hubers1: no visible global function definition for ‘pnorm’
normQA: no visible binding for global variable ‘group’
normQA: no visible binding for global variable ‘hasPeak’
pcout: no visible global function definition for ‘qchisq’
singletGate: no visible global function definition for ‘predict’
symconv.ks: no visible global function definition for ‘fft’
symconv2D.ks: no visible global function definition for ‘fft’
symconv3D.ks: no visible global function definition for ‘fft’
symconv4D.ks: no visible global function definition for ‘fft’
warpSetNCDF: no visible global function definition for
‘clone.ncdfFlowSet’
warpSetNCDFLowMem: no visible global function definition for
‘clone.ncdfFlowSet’
addName,curv1Filter-character: no visible global function definition
for ‘checkParameterMatch’
addName,curv2Filter-character: no visible global function definition
for ‘checkParameterMatch’
glines,curv1Filter-ANY: no visible global function definition for
‘evalError’
glines,curv1Filter-missing: no visible global function definition for
‘evalError’
glines,curv1Filter-multipleFilterResult: no visible global function
definition for ‘colorRampPalette’
glines,curv1Filter-multipleFilterResult: no visible global function
definition for ‘brewer.pal’
glines,curv2Filter-ANY: no visible global function definition for
‘evalError’
glines,curv2Filter-multipleFilterResult: no visible global function
definition for ‘colorRampPalette’
glines,curv2Filter-multipleFilterResult: no visible global function
definition for ‘brewer.pal’
glpoints,curv1Filter-flowFrame-character: no visible global function
definition for ‘multFiltPoints’
glpoints,curv2Filter-flowFrame-character: no visible global function
definition for ‘multFiltPoints’
glpolygon,curv1Filter-ANY: no visible global function definition for
‘evalError’
glpolygon,curv2Filter-ANY: no visible global function definition for
‘evalError’
gpoints,curv1Filter-flowFrame-character: no visible global function
definition for ‘checkParameterMatch’
gpoints,curv1Filter-flowFrame-character: no visible global function
definition for ‘colorRampPalette’
gpoints,curv1Filter-flowFrame-character: no visible global function
definition for ‘brewer.pal’
gpoints,curv2Filter-flowFrame-character: no visible global function
definition for ‘checkParameterMatch’
gpoints,curv2Filter-flowFrame-character: no visible global function
definition for ‘colorRampPalette’
gpoints,curv2Filter-flowFrame-character: no visible global function
definition for ‘brewer.pal’
gpolygon,curv1Filter-ANY: no visible global function definition for
‘evalError’
gpolygon,curv1Filter-missing: no visible global function definition for
‘evalError’
gpolygon,curv1Filter-multipleFilterResult: no visible global function
definition for ‘colorRampPalette’
gpolygon,curv1Filter-multipleFilterResult: no visible global function
definition for ‘brewer.pal’
gpolygon,curv2Filter-ANY: no visible global function definition for
‘evalError’
gpolygon,curv2Filter-multipleFilterResult: no visible global function
definition for ‘colorRampPalette’
gpolygon,curv2Filter-multipleFilterResult: no visible global function
definition for ‘brewer.pal’
summarizeFilter,multipleFilterResult-curv1Filter: no visible global
function definition for ‘callNextMethod’
summarizeFilter,multipleFilterResult-curv2Filter: no visible global
function definition for ‘callNextMethod’
Undefined global functions or variables:
IQR bogus brewer.pal callNextMethod checkParameterMatch
clone.ncdfFlowSet cluster colorRampPalette evalError fft group
hasPeak multFiltPoints norder.bspline params pchisq pnorm predict
qchisq whichS y
Consider adding
importFrom("grDevices", "colorRampPalette")
importFrom("methods", "callNextMethod")
importFrom("stats", "IQR", "fft", "pchisq", "pnorm", "predict",
"qchisq")
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 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
warpSet 23.434 5.254 29.012
gaussNorm 11.447 0.502 12.164
density1d 5.002 0.433 5.543
lymphGate 5.102 0.261 5.415
* 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 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/flowStats.Rcheck/00check.log’
for details.
* installing *source* package ‘flowStats’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (flowStats)