Package: sigaR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sigaR_1.4.0.tar.gz

StartedAt: 2013-05-01 10:54:37 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 11:03:08 -0700 (Wed, 01 May 2013)

EllapsedTime: 510.7 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/sigaR.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'sigaR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sigaR' version '1.4.0'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'sigaR' can be installed ... [9s/10s] OK
* checking installed package size ... OK
* checking package 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
* 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 installed files from 'inst/doc' ... OK
* checking examples ... [387s/395s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     291.788 32.643 331.371
cisEffectTune   27.193  0.296  27.635
pathway2sample   5.967  1.384   7.478
RCMtest          6.484  0.028   6.804
* 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-2.12-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
** testing if installed package can be loaded
* DONE (sigaR)

name	user	system	elapsed
CNGEheatmaps	1.703	0.052	1.815
ExpressionSet2order	0.025	0.001	0.027
ExpressionSet2subset	0.023	0.002	0.024
ExpressionSet2weightedSubset	0.323	0.014	0.338
RCMestimation	1.751	0.040	1.828
RCMrandom	1.750	0.017	1.786
RCMtest	6.484	0.028	6.804
cghCall2cghSeg	0.092	0.002	0.097
cghCall2maximumSubset	0.556	0.024	0.586
cghCall2order	0.033	0.003	0.035
cghCall2subset	0.108	0.005	0.113
cghCall2weightedSubset	0.532	0.011	0.543
cghSeg2order	0.110	0.002	0.113
cghSeg2subset	0.139	0.002	0.141
cghSeg2weightedSubset	0.377	0.007	0.385
cisEffectPlot	0.128	0.004	0.136
cisEffectTable	2.967	0.082	3.084
cisEffectTest	2.752	0.077	2.844
cisEffectTune	27.193	0.296	27.635
cisTest-class	0.009	0.000	0.011
entTest-class	0.011	0.001	0.012
entropyTest	0.285	0.003	0.298
expandMatching2singleIDs	0.091	0.006	0.097
getSegFeatures	0.023	0.003	0.027
hdEntropy	0.025	0.002	0.027
hdMI	0.548	0.003	0.552
matchAnn2Ann	0.073	0.006	0.078
matchCGHcall2ExpressionSet	0.096	0.004	0.101
merge2ExpressionSets	0.108	0.001	0.110
merge2cghCalls	0.148	0.004	0.151
miTest-class	0.006	0.002	0.008
mutInfTest	291.788	32.643	331.371
nBreakpoints	0.412	0.018	0.432
pathway1sample	0.238	0.041	0.280
pathway2sample	5.967	1.384	7.478
pathwayFit-class	0.003	0.005	0.008
pathwayPlot	0.190	0.053	0.258
pollackCN16	0.009	0.005	0.014
pollackGE16	0.005	0.005	0.011
profilesPlot	0.223	0.018	0.266
rcmFit-class	0.003	0.004	0.009
rcmTest-class	0.003	0.004	0.007
splitMatchingAtBreakpoints	0.415	0.023	0.446
uniqGenomicInfo	0.014	0.008	0.023