Charles Berry
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/geneRxCluster |
| Branch: RELEASE_3_7 |
| Last Commit: 69c5cb2 |
| Last Changed Date: 2018-04-30 10:35:32 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:38:04 -0400 (Wed, 17 Oct 2018).
| Package 575/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| geneRxCluster 1.16.0 Charles Berry
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: geneRxCluster |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneRxCluster.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings geneRxCluster_1.16.0.tar.gz |
| StartedAt: 2018-10-17 02:12:23 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 02:14:16 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 112.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: geneRxCluster.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneRxCluster.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings geneRxCluster_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/geneRxCluster.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geneRxCluster/DESCRIPTION' ... OK
* this is package 'geneRxCluster' version '1.16.0'
* 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 'geneRxCluster' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.gRxCluster: no visible global function definition for 'tail'
.gRxCluster: no visible global function definition for 'head'
.gRxCluster: no visible global function definition for 'metadata'
.gRxCluster: no visible global function definition for 'metadata<-'
critVal.alpha : <anonymous>: no visible global function definition for
'pbinom'
critVal.alpha : <anonymous>: no visible global function definition for
'tail'
critVal.alpha : <anonymous>: no visible global function definition for
'head'
critVal.power: no visible global function definition for 'plogis'
critVal.power: no visible global function definition for 'qlogis'
critVal.power : <anonymous>: no visible global function definition for
'qbinom'
critVal.power : <anonymous>: no visible global function definition for
'dbinom'
critVal.power : <anonymous>: no visible global function definition for
'pbinom'
critVal.target : <anonymous>: no visible global function definition for
'pbinom'
critVal.target : <anonymous>: no visible global function definition for
'tail'
critVal.target : <anonymous>: no visible global function definition for
'head'
gRxCluster: no visible global function definition for 'as'
gRxCluster: no visible global function definition for 'runValue'
gRxCluster: no visible global function definition for 'metadata'
gRxCluster: no visible global function definition for 'metadata<-'
gRxPlot: no visible global function definition for 'qlogis'
gRxPlot: no visible global function definition for 'hist'
gRxPlot: no visible global function definition for 'plot'
gRxPlot: no visible global function definition for 'metadata'
gRxPlotClumps: no visible global function definition for 'metadata'
gRxPlotClumps: no visible global function definition for 'seqlengths'
gRxPlotClumps: no visible global function definition for 'runValue'
gRxPlotClumps: no visible global function definition for 'seqlengths<-'
gRxPlotClumps: no visible global function definition for 'queryHits'
gRxPlotClumps: no visible global function definition for 'subjectHits'
gRxPlotClumps: no visible global function definition for 'par'
gRxPlotClumps: no visible global function definition for 'plot'
gRxPlotClumps: no visible global function definition for 'box'
gRxPlotClumps: no visible global function definition for 'segments'
gRxPlotClumps: no visible global function definition for 'text'
gRxSummary: no visible global function definition for 'metadata'
plot.cutpoints: no visible global function definition for 'barplot'
plot.cutpoints: no visible global function definition for 'points'
prune.loglik : x.max: no visible global function definition for
'subjectHits'
Undefined global functions or variables:
as barplot box dbinom head hist metadata metadata<- par pbinom plogis
plot points qbinom qlogis queryHits runValue segments seqlengths
seqlengths<- subjectHits tail text
Consider adding
importFrom("graphics", "barplot", "box", "hist", "par", "plot",
"points", "segments", "text")
importFrom("methods", "as")
importFrom("stats", "dbinom", "pbinom", "plogis", "qbinom", "qlogis")
importFrom("utils", "head", "tail")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/geneRxCluster/libs/i386/geneRxCluster.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'doRunit.R'
OK
** running tests for arch 'x64' ...
Running 'doRunit.R'
OK
* 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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/geneRxCluster.Rcheck/00check.log'
for details.
geneRxCluster.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/geneRxCluster_1.16.0.tar.gz && rm -rf geneRxCluster.buildbin-libdir && mkdir geneRxCluster.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geneRxCluster.buildbin-libdir geneRxCluster_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL geneRxCluster_1.16.0.zip && rm geneRxCluster_1.16.0.tar.gz geneRxCluster_1.16.0.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 26467 100 26467 0 0 479k 0 --:--:-- --:--:-- --:--:-- 549k
install for i386
* installing *source* package 'geneRxCluster' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c cluster.c -o cluster.o
cluster.c: In function 'cutptClean_new_elt':
cluster.c:80:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (*pvj!=NOTAIL)
^
cluster.c: In function 'gRxC_cluster':
cluster.c:682:2: warning: 'cutptFunRes' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(final,2,cutptFunRes);
^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o geneRxCluster.dll tmp.def cluster.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/geneRxCluster.buildbin-libdir/geneRxCluster/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'geneRxCluster'
finding HTML links ... done
critVal.alpha html
critVal.power html
critVal.target html
gRxCluster-object html
finding level-2 HTML links ... done
gRxCluster html
gRxPlot html
gRxPlotClumps html
gRxSummary html
geneRxCluster html
noprune html
plot.cutpoints html
prune.loglik html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'geneRxCluster' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c cluster.c -o cluster.o
cluster.c: In function 'cutptClean_new_elt':
cluster.c:80:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
if (*pvj!=NOTAIL)
^
cluster.c: In function 'gRxC_cluster':
cluster.c:682:2: warning: 'cutptFunRes' may be used uninitialized in this function [-Wmaybe-uninitialized]
SET_VECTOR_ELT(final,2,cutptFunRes);
^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o geneRxCluster.dll tmp.def cluster.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/geneRxCluster.buildbin-libdir/geneRxCluster/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geneRxCluster' as geneRxCluster_1.16.0.zip
* DONE (geneRxCluster)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'geneRxCluster' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
geneRxCluster.Rcheck/tests_i386/doRunit.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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.
> ## unit tests will not be done if RUnit is not available
> if(require("RUnit", quietly=TRUE)) {
+
+ ## --- Setup ---
+
+ pkg <- "geneRxCluster" # <-- Change to package name!
+ if(Sys.getenv("RCMDCHECK") == "FALSE") {
+ ## Path to unit tests for standalone running under Makefile (not R CMD check)
+ ## PKG/tests/../inst/unitTests
+ path <- file.path(getwd(), "..", "inst", "unitTests")
+ } else {
+ ## Path to unit tests for R CMD check
+ ## PKG.Rcheck/tests/../PKG/unitTests
+ path <- system.file(package=pkg, "unitTests")
+ }
+ cat("\nRunning unit tests\n")
+ print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
+
+ library(package=pkg, character.only=TRUE)
+
+ ## If desired, load the name space to allow testing of private functions
+ ## if (is.element(pkg, loadedNamespaces()))
+ ## attach(loadNamespace(pkg), name=paste("namespace", pkg, sep=":"), pos=3)
+ ##
+ ## or simply call PKG:::myPrivateFunction() in tests
+
+ ## --- Testing ---
+
+ ## Define tests
+ testSuite <- defineTestSuite(name=paste(pkg, "unit testing"),
+ dirs=path)
+ ## Run
+ tests <- runTestSuite(testSuite)
+
+ ## Default report name
+ pathReport <- file.path(path, "report")
+
+ ## Report to stdout and text files
+ cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
+ printTextProtocol(tests, showDetails=FALSE)
+ printTextProtocol(tests, showDetails=FALSE,
+ fileName=paste(pathReport, "Summary.txt", sep=""))
+ printTextProtocol(tests, showDetails=TRUE,
+ fileName=paste(pathReport, ".txt", sep=""))
+
+ ## Report to HTML file
+ printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep=""))
+
+ ## Return stop() to cause R CMD check stop in case of
+ ## - failures i.e. FALSE to unit tests or
+ ## - errors i.e. R errors
+ tmp <- getErrors(tests)
+ if(tmp$nFail > 0 | tmp$nErr > 0) {
+ stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail,
+ ", #R errors: ", tmp$nErr, ")\n\n", sep=""))
+ }
+ } else {
+ warning("cannot run unit tests -- package RUnit is not available")
+ }
Running unit tests
$pkg
[1] "geneRxCluster"
$getwd
[1] "C:/Users/biocbuild/bbs-3.7-bioc/meat/geneRxCluster.Rcheck/tests_i386"
$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.7-bioc/R/library/geneRxCluster/unitTests"
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Executing test function test_bad_args_gRxCluster ... Error in gRxCluster(rep("a", 100), 0:100L, c(rep(TRUE, 5), rep(c(FALSE, :
object, starts, and group must have same lengths
done successfully.
Executing test function test_crossover_gRxCluster ... done successfully.
Executing test function test_permutation_both_ways_gRxCluster ... done successfully.
Executing test function test_prune_gRxCluster ... done successfully.
Executing test function test_simply_grx_clust_Call ... done successfully.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Wed Oct 17 02:14:05 2018
***********************************************
Number of test functions: 5
Number of errors: 0
Number of failures: 0
1 Test Suite :
geneRxCluster unit testing - 5 test functions, 0 errors, 0 failures
>
> proc.time()
user system elapsed
4.42 0.20 4.64
|
geneRxCluster.Rcheck/tests_x64/doRunit.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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.
> ## unit tests will not be done if RUnit is not available
> if(require("RUnit", quietly=TRUE)) {
+
+ ## --- Setup ---
+
+ pkg <- "geneRxCluster" # <-- Change to package name!
+ if(Sys.getenv("RCMDCHECK") == "FALSE") {
+ ## Path to unit tests for standalone running under Makefile (not R CMD check)
+ ## PKG/tests/../inst/unitTests
+ path <- file.path(getwd(), "..", "inst", "unitTests")
+ } else {
+ ## Path to unit tests for R CMD check
+ ## PKG.Rcheck/tests/../PKG/unitTests
+ path <- system.file(package=pkg, "unitTests")
+ }
+ cat("\nRunning unit tests\n")
+ print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
+
+ library(package=pkg, character.only=TRUE)
+
+ ## If desired, load the name space to allow testing of private functions
+ ## if (is.element(pkg, loadedNamespaces()))
+ ## attach(loadNamespace(pkg), name=paste("namespace", pkg, sep=":"), pos=3)
+ ##
+ ## or simply call PKG:::myPrivateFunction() in tests
+
+ ## --- Testing ---
+
+ ## Define tests
+ testSuite <- defineTestSuite(name=paste(pkg, "unit testing"),
+ dirs=path)
+ ## Run
+ tests <- runTestSuite(testSuite)
+
+ ## Default report name
+ pathReport <- file.path(path, "report")
+
+ ## Report to stdout and text files
+ cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
+ printTextProtocol(tests, showDetails=FALSE)
+ printTextProtocol(tests, showDetails=FALSE,
+ fileName=paste(pathReport, "Summary.txt", sep=""))
+ printTextProtocol(tests, showDetails=TRUE,
+ fileName=paste(pathReport, ".txt", sep=""))
+
+ ## Report to HTML file
+ printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep=""))
+
+ ## Return stop() to cause R CMD check stop in case of
+ ## - failures i.e. FALSE to unit tests or
+ ## - errors i.e. R errors
+ tmp <- getErrors(tests)
+ if(tmp$nFail > 0 | tmp$nErr > 0) {
+ stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail,
+ ", #R errors: ", tmp$nErr, ")\n\n", sep=""))
+ }
+ } else {
+ warning("cannot run unit tests -- package RUnit is not available")
+ }
Running unit tests
$pkg
[1] "geneRxCluster"
$getwd
[1] "C:/Users/biocbuild/bbs-3.7-bioc/meat/geneRxCluster.Rcheck/tests_x64"
$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.7-bioc/R/library/geneRxCluster/unitTests"
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
Executing test function test_bad_args_gRxCluster ... Error in gRxCluster(rep("a", 100), 0:100L, c(rep(TRUE, 5), rep(c(FALSE, :
object, starts, and group must have same lengths
done successfully.
Executing test function test_crossover_gRxCluster ... done successfully.
Executing test function test_permutation_both_ways_gRxCluster ... done successfully.
Executing test function test_prune_gRxCluster ... done successfully.
Executing test function test_simply_grx_clust_Call ... done successfully.
------------------- UNIT TEST SUMMARY ---------------------
RUNIT TEST PROTOCOL -- Wed Oct 17 02:14:10 2018
***********************************************
Number of test functions: 5
Number of errors: 0
Number of failures: 0
1 Test Suite :
geneRxCluster unit testing - 5 test functions, 0 errors, 0 failures
>
> proc.time()
user system elapsed
5.20 0.21 5.40
|
|
geneRxCluster.Rcheck/examples_i386/geneRxCluster-Ex.timings
|
geneRxCluster.Rcheck/examples_x64/geneRxCluster-Ex.timings
|