Mike Jiang
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/flowViz |
| Branch: RELEASE_3_12 |
| Last Commit: f80fd24 |
| Last Changed Date: 2020-10-27 10:29:52 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:31:21 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the flowViz package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 639/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowViz 1.54.0 (landing page) Mike Jiang
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: flowViz |
| Version: 1.54.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowViz.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings flowViz_1.54.0.tar.gz |
| StartedAt: 2021-05-06 02:53:44 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:57:27 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 223.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flowViz.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowViz.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings flowViz_1.54.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/flowViz.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowViz' version '1.54.0'
* 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 whether package 'flowViz' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glines-methods.Rd:87: file link 'kmeansFilter' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glines-methods.Rd:99: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glines-methods.Rd:106: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glines-methods.Rd:113: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glines-methods.Rd:120: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glpolygon-methods.Rd:118: file link 'kmeansFilter' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glpolygon-methods.Rd:130: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glpolygon-methods.Rd:137: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glpolygon-methods.Rd:144: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glpolygon-methods.Rd:151: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/gpolygon-methods.Rd:111: file link 'kmeansFilter' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/gpolygon-methods.Rd:123: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/gpolygon-methods.Rd:130: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/gpolygon-methods.Rd:137: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/gpolygon-methods.Rd:144: file link 'ellipsoidGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/xyplot.Rd:115: file link 'filtersList-class' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/xyplot.Rd:185: file link 'sqrt' in package 'base' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/flowViz.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' '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:
'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
.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'
densityplot,formula-ncdfFlowList: no visible global function definition
for 'selectMethod'
densityplot,formula-view: no visible global function definition for
'Data'
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'
histogram,formula-ncdfFlowList: no visible global function definition
for 'selectMethod'
xyplot,formula-gateView: no visible global function definition for
'action'
xyplot,formula-gateView: no visible global function definition for
'Data'
xyplot,formula-gateView: no visible global function definition for
'parent'
xyplot,formula-ncdfFlowList: no visible global function definition for
'selectMethod'
xyplot,formula-view: no visible global function definition for 'Data'
xyplot,view-missing: no visible global function definition for 'Data'
Undefined global functions or variables:
Data action as.formula contourLines densCols extends fd filterResult
parent parms rainbow rl selectMethod strict
Consider adding
importFrom("grDevices", "contourLines", "densCols", "rainbow")
importFrom("methods", "extends", "selectMethod")
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:150-152: 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' ... NOTE
Files named as vignettes but with no recognized vignette engine:
'vignettes/densityplot_vs_histogram.Rmd'
(Is a VignetteBuilder field missing?)
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
xyplot 10.61 0.22 10.84
densityplot 10.10 0.47 10.57
splom 10.16 0.36 10.52
lattice-methods 9.25 0.42 9.68
timeLinePlot 6.34 0.09 6.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
densityplot 10.52 0.47 10.98
splom 10.69 0.23 10.92
xyplot 10.05 0.11 10.15
lattice-methods 9.73 0.30 10.03
timeLinePlot 7.00 0.10 7.10
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* 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 WARNING, 6 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/flowViz.Rcheck/00check.log'
for details.
flowViz.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/flowViz_1.54.0.tar.gz && rm -rf flowViz.buildbin-libdir && mkdir flowViz.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowViz.buildbin-libdir flowViz_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL flowViz_1.54.0.zip && rm flowViz_1.54.0.tar.gz flowViz_1.54.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 805k 100 805k 0 0 31.2M 0 --:--:-- --:--:-- --:--:-- 32.7M
install for i386
* installing *source* package 'flowViz' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
in method for 'densityplot' with signature 'x="formula",data="view"': no definition for class "view"
in method for 'densityplot' with signature 'x="formula",data="ncdfFlowSet"': no definition for class "ncdfFlowSet"
in method for 'densityplot' with signature 'x="formula",data="ncdfFlowList"': no definition for class "ncdfFlowList"
in method for 'histogram' with signature 'x="formula",data="ncdfFlowSet"': no definition for class "ncdfFlowSet"
in method for 'histogram' with signature 'x="formula",data="ncdfFlowList"': no definition for class "ncdfFlowList"
in method for 'glines' with signature 'x="norm2Filter",data="ANY"': no definition for class "norm2Filter"
in method for 'glines' with signature 'x="norm2Filter",data="logicalFilterResult"': no definition for class "norm2Filter"
in method for 'glines' with signature 'x="norm2Filter",data="flowFrame"': no definition for class "norm2Filter"
in method for 'glpoints' with signature 'x="norm2Filter",data="flowFrame",channels="character"': no definition for class "norm2Filter"
in method for 'glpolygon' with signature 'x="norm2Filter",data="ANY"': no definition for class "norm2Filter"
in method for 'glpolygon' with signature 'x="norm2Filter",data="logicalFilterResult"': no definition for class "norm2Filter"
in method for 'glpolygon' with signature 'x="norm2Filter",data="flowFrame"': no definition for class "norm2Filter"
in method for 'gpoints' with signature 'x="norm2Filter",data="flowFrame",channels="character"': no definition for class "norm2Filter"
in method for 'gpolygon' with signature 'x="norm2Filter",data="ANY"': no definition for class "norm2Filter"
in method for 'gpolygon' with signature 'x="norm2Filter",data="logicalFilterResult"': no definition for class "norm2Filter"
in method for 'gpolygon' with signature 'x="norm2Filter",data="flowFrame"': no definition for class "norm2Filter"
in method for 'xyplot' with signature 'x="formula",data="view"': no definition for class "view"
in method for 'xyplot' with signature 'x="view",data="missing"': no definition for class "view"
in method for 'xyplot' with signature 'x="formula",data="gateView"': no definition for class "gateView"
in method for 'xyplot' with signature 'x="formula",data="ncdfFlowSet"': no definition for class "ncdfFlowSet"
in method for 'xyplot' with signature 'x="formula",data="ncdfFlowList"': no definition for class "ncdfFlowList"
** help
*** installing help indices
converting help for package 'flowViz'
finding HTML links ... done
addName-methods html
contour-methods html
densityplot html
dot-process_flowFrame_overlay html
dot-process_overlay_flowSet html
ecdfplot html
flowPlot html
flowViz-package html
flowViz.par.get html
glines-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glines-methods.Rd:87: file link 'kmeansFilter' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glines-methods.Rd:99: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glines-methods.Rd:106: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glines-methods.Rd:113: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glines-methods.Rd:120: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
glpoints-methods html
glpolygon-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glpolygon-methods.Rd:118: file link 'kmeansFilter' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glpolygon-methods.Rd:130: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glpolygon-methods.Rd:137: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glpolygon-methods.Rd:144: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/glpolygon-methods.Rd:151: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
gpoints-methods html
gpolygon-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/gpolygon-methods.Rd:111: file link 'kmeansFilter' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/gpolygon-methods.Rd:123: file link 'polygonGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/gpolygon-methods.Rd:130: file link 'quadGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/gpolygon-methods.Rd:137: file link 'rectangleGate' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/gpolygon-methods.Rd:144: file link 'ellipsoidGate' in package 'flowCore' does not exist and so has been treated as a topic
lattice-methods html
plot html
splom html
timeLinePlot html
xyplot html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/xyplot.Rd:115: file link 'filtersList-class' in package 'flowCore' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/Rtmpsl22iS/R.INSTALLe247edf75c4/flowViz/man/xyplot.Rd:185: file link 'sqrt' in package 'base' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
'filters.Rmd'
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'flowViz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowViz' as flowViz_1.54.0.zip
* DONE (flowViz)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'flowViz' successfully unpacked and MD5 sums checked
|
flowViz.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(flowViz)
Loading required package: flowCore
Loading required package: lattice
>
> test_check("flowViz")
[ FAIL 0 | WARN 36 | SKIP 0 | PASS 9 ]
>
> proc.time()
user system elapsed
7.40 0.35 7.75
|
flowViz.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(flowViz)
Loading required package: flowCore
Loading required package: lattice
>
> test_check("flowViz")
[ FAIL 0 | WARN 36 | SKIP 0 | PASS 9 ]
>
> proc.time()
user system elapsed
6.98 0.48 7.46
|
|
flowViz.Rcheck/examples_i386/flowViz-Ex.timings
|
flowViz.Rcheck/examples_x64/flowViz-Ex.timings
|