flowStats 3.24.8
Greg Finak and Mike Jiang
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/flowStats | | Last Changed Rev: 97532 / Revision: 102249 | | Last Changed Date: 2014-12-10 10:19:14 -0800 (Wed, 10 Dec 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | 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 --no-multiarch flowStats_3.24.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/flowStats.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘3.24.8’
* 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 ... [25s/28s] 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’
glpolygon,curv1Filter-ANY: no visible global function definition for
‘evalError’
glpolygon,curv2Filter-ANY: no visible global function definition for
‘evalError’
* 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 ... [126s/126s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
warpSet 38.408 8.359 46.823
gaussNorm 11.859 0.948 12.908
lymphGate 10.263 0.688 10.972
density1d 8.610 0.709 9.401
rangeGate 5.869 0.659 6.751
autoGate 6.303 0.181 6.495
gpaSet 5.987 0.394 6.408
* 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
NOTE: There were 3 notes.
See
‘/Users/biocbuild/bbs-3.0-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 in fun(libname, pkgname) : error in rgl_init
** 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 in fun(libname, pkgname) : error in rgl_init
* DONE (flowStats)