flowQ 1.29.0
Mike Jiang
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowQ | | Last Changed Rev: 102594 / Revision: 107696 | | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | 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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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowQ_1.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/flowQ.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 ‘flowQ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowQ’ version ‘1.29.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘outliers’ ‘lattice’ ‘flowViz’ ‘mvoutlier’ ‘bioDist’
‘parody’ ‘RColorBrewer’ ‘latticeExtra’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowQ’ can be installed ... [13s/14s] 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:
‘methods’ ‘BiocGenerics’ ‘flowViz’
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
'library' or 'require' call to ‘lattice’ which was already attached by Depends.
Please remove these calls from your code.
Namespace in Imports field not imported from: ‘IRanges’
All declared Imports should be used.
Packages in Depends field not imported from:
‘RColorBrewer’ ‘bioDist’ ‘flowViz’ ‘lattice’ ‘latticeExtra’
‘mvoutlier’ ‘outliers’ ‘parody’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
‘flowCore:::copyFlowSet’ ‘flowCore:::findTimeChannel’
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
evaluateProcess: multiple local function definitions for ‘efun’ with
different formal arguments
failedProcesses: no visible global function definition for ‘listLen’
normalizeSets : <anonymous>: no visible global function definition for
‘warpSet’
outlierD : <anonymous>: no visible global function definition for
‘dixon.test’
outlierG : <anonymous>: no visible global function definition for
‘grubbs.test’
outlierX2 : <anonymous>: no visible global function definition for
‘chisq.out.test’
qaProcess.2DStatsPlot: no visible global function definition for
‘brewer.pal’
qaProcess.2DStatsPlot: no visible global function definition for
‘pcout’
qaProcess.2DStatsPlot: no visible global function definition for
‘xyplot’
qaProcess.2DStatsPlot: no visible binding for global variable ‘Aliquot’
qaProcess.2DStatsPlot: no visible global function definition for
‘simpleKey’
qaProcess.BoundaryPlot: no visible global function definition for
‘brewer.pal’
qaProcess.BoundaryPlot: no visible global function definition for
‘barchart’
qaProcess.BoundaryPlot: no visible global function definition for
‘simpleKey’
qaProcess.DensityPlot: no visible global function definition for
‘brewer.pal’
qaProcess.DensityPlot: no visible global function definition for
‘KLdist.matrix’
qaProcess.DensityPlot: no visible global function definition for
‘xyplot’
qaProcess.DensityPlot: no visible binding for global variable ‘Aliquot’
qaProcess.DensityPlot: no visible global function definition for
‘simpleKey’
qaProcess.DensityPlot: no visible global function definition for
‘densityplot’
qaProcess.DensityPlot : <anonymous>: no visible binding for global
variable ‘panel.xyplot’
qaProcess.DensityPlot : <anonymous>: no visible global function
definition for ‘trellis.panelArgs’
qaProcess.DensityPlot: no visible global function definition for
‘calout.detect’
qaProcess.ECDFPlot: no visible global function definition for
‘brewer.pal’
qaProcess.ECDFPlot: no visible global function definition for ‘xyplot’
qaProcess.ECDFPlot: no visible binding for global variable ‘Aliquot’
qaProcess.ECDFPlot: no visible global function definition for
‘simpleKey’
qaProcess.ECDFPlot: no visible global function definition for
‘KLdist.matrix’
qaProcess.ECDFPlot: no visible global function definition for
‘ecdfplot’
qaProcess.ECDFPlot: no visible global function definition for
‘densityplot’
qaProcess.ECDFPlot : <anonymous>: no visible binding for global
variable ‘panel.xyplot’
qaProcess.ECDFPlot : <anonymous>: no visible global function definition
for ‘trellis.panelArgs’
qaProcess.ECDFPlot: no visible global function definition for
‘calout.detect’
qaProcess.KLDistPlot: no visible global function definition for
‘brewer.pal’
qaProcess.KLDistPlot: no visible global function definition for
‘KLdist.matrix’
qaProcess.KLDistPlot: no visible global function definition for
‘levelplot’
qaProcess.KLDistPlot: no visible global function definition for
‘calout.detect’
qaProcess.marginevents: no visible global function definition for
‘levelplot’
qaProcess.timeflow: no visible global function definition for
‘timeLinePlot’
qaProcess.timeline: no visible global function definition for
‘timeLinePlot’
outliers,flowSet : .local: no visible binding for global variable
‘variance’
* checking Rd files ... NOTE
prepare_Rd: normalizeSets.Rd:44-51: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'qaProcess.timeflow.Rd':
‘[flowViz:timeLinePlot-methods]{timeLinePlot}’
Missing link or links in documentation object 'qaProcess.timeline.Rd':
‘[flowViz:timeLinePlot-methods]{timeLinePlot}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... [59s/61s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
qaProcess.2DStatsPlot 12.172 0.673 13.867
qaProcess.DensityPlot 9.791 0.390 10.926
qaProcess.ECDFPlot 9.395 0.369 9.933
qaProcess.KLDistPlot 9.380 0.368 9.934
qaProcess.BoundaryPlot 6.330 0.338 6.721
* 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, 6 NOTEs
See
‘/Users/biocbuild/bbs-3.2-bioc/meat/flowQ.Rcheck/00check.log’
for details.