Package: sigaR

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sigaR_1.0.0.tar.gz

StartedAt: 2012-09-24 01:43:17 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 01:49:59 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 401.6 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/sigaR.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.0.0'
* 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 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
CNGEheatmaps: warning in layout(matrix(c(1, 2, 3, 1, 2, 3, 1, 2, 3), 3,
  3, byrow = TRUE), width = c(1, 9, 9)): partial argument match of
  'width' to 'widths'
hdEntropy : normEntropy: warning in round(lambda, d = 5): partial
  argument match of 'd' to 'digits'
hdMI : normMI: warning in round(lambda, d = 5): partial argument match
  of 'd' to 'digits'
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'
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-2.10-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	1.851	0.054	1.907
ExpressionSet2order	0.027	0.004	0.030
ExpressionSet2subset	0.015	0.001	0.017
ExpressionSet2weightedSubset	0.307	0.005	0.313
RCMestimation	2.177	0.011	2.187
RCMrandom	2.237	0.005	2.242
RCMtest	8.236	0.009	8.244
cghCall2maximumSubset	0.622	0.015	0.637
cghCall2order	0.040	0.005	0.044
cghCall2subset	0.106	0.003	0.109
cghCall2weightedSubset	0.436	0.014	0.450
entTest-class	0.001	0.001	0.001
entropyTest	0.241	0.009	0.250
expandMatching2singleIDs	0.099	0.003	0.102
getSegFeatures	0.016	0.001	0.018
hdEntropy	0.027	0.002	0.029
hdMI	0.366	0.005	0.370
matchAnn2Ann	0.083	0.003	0.086
matchCGHcall2ExpressionSet	0.120	0.006	0.126
merge2ExpressionSets	0.126	0.002	0.128
merge2cghCalls	0.177	0.005	0.183
miTest-class	0.001	0.000	0.000
mutInfTest	219.324	63.682	287.209
nBreakpoints	0.297	0.006	0.305
pollackCN16	0.008	0.001	0.010
pollackGE16	0.004	0.001	0.005
profilesPlot	0.170	0.007	0.177
rcmFit-class	0.000	0.001	0.001
rcmTest-class	0.001	0.000	0.001
splitMatchingAtBreakpoints	0.303	0.004	0.308
uniqGenomicInfo	0.009	0.001	0.011