Package: sigaR

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sigaR_1.1.1.tar.gz

StartedAt: 2012-06-21 03:36:00 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 03:45:12 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 551.5 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/sigaR.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'sigaR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sigaR' version '1.1.1'
* 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 whether package 'sigaR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated 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
ExpressionSet2weightedSubset: no visible binding for global variable
  'sigaR'
RCMestimation : RCMmlH2: multiple local function definitions for
  'tau.estimator' with different formal arguments
RCMtest: no visible binding for global variable 'sigaR'
RCMtest: no visible binding for global variable 'quadprog'
RCMtest: no visible binding for global variable 'MASS'
cghCall2maximumSubset: no visible binding for global variable 'sigaR'
cghCall2weightedSubset: no visible binding for global variable 'sigaR'
cghSeg2weightedSubset: no visible binding for global variable 'sigaR'
entropyTest: no visible binding for global variable 'sigaR'
entropyTest: no visible binding for global variable 'corpcor'
matchAnn2Ann: no visible binding for global variable 'sigaR'
matchCGHcall2ExpressionSet: no visible binding for global variable
  'sigaR'
mutInfTest: no visible binding for global variable 'sigaR'
mutInfTest: no visible binding for global variable 'corpcor'
* 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 examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/sigaR.Rcheck/00check.log'
for details.

* installing *source* package 'sigaR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'sigaR.Rnw' 
** testing if installed package can be loaded

* DONE (sigaR)

name	user	system	elapsed
CNGEheatmaps	1.760	0.044	1.813
ExpressionSet2order	0.018	0.002	0.021
ExpressionSet2subset	0.014	0.003	0.017
ExpressionSet2weightedSubset	0.273	0.007	0.280
RCMestimation	1.834	0.013	1.859
RCMrandom	1.854	0.006	1.868
RCMtest	7.029	0.017	7.130
cghCall2cghSeg	0.093	0.002	0.096
cghCall2maximumSubset	0.540	0.018	0.567
cghCall2order	0.031	0.005	0.036
cghCall2subset	0.089	0.003	0.094
cghCall2weightedSubset	0.378	0.012	0.399
cghSeg2order	0.095	0.004	0.099
cghSeg2subset	0.145	0.003	0.149
cghSeg2weightedSubset	0.412	0.007	0.421
cisEffectPlot	0.129	0.005	0.136
cisEffectTable	3.463	0.073	3.616
cisEffectTest	3.477	0.067	3.577
cisEffectTune	27.735	0.217	28.507
cisTest-class	0.001	0.001	0.002
entTest-class	0.001	0.000	0.002
entropyTest	0.220	0.011	0.232
expandMatching2singleIDs	0.085	0.004	0.098
getSegFeatures	0.014	0.002	0.016
hdEntropy	0.019	0.002	0.022
hdMI	0.352	0.005	0.360
matchAnn2Ann	0.072	0.003	0.075
matchCGHcall2ExpressionSet	0.103	0.006	0.109
merge2ExpressionSets	0.115	0.003	0.135
merge2cghCalls	0.158	0.008	0.189
miTest-class	0.001	0.000	0.001
mutInfTest	286.896	91.260	392.416
nBreakpoints	0.433	0.009	0.448
pollackCN16	0.008	0.002	0.010
pollackGE16	0.003	0.001	0.005
profilesPlot	0.230	0.011	0.245
rcmFit-class	0.001	0.001	0.001
rcmTest-class	0.001	0.000	0.001
splitMatchingAtBreakpoints	0.429	0.005	0.436
uniqGenomicInfo	0.013	0.001	0.015