Package: sigaR

Version: 1.2.1

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.2.1.tar.gz

StartedAt: 2013-03-25 04:52:37 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:59:16 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 399.0 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/sigaR.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sigaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sigaR’ version ‘1.2.1’
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     201.689  8.320 235.112
cisEffectTune   19.085  0.020  21.968
pathway2sample   6.160  2.008   9.240
RCMtest          5.004  0.016   5.998
* 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
  ‘/loc/home/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	1.404	0.032	1.868
ExpressionSet2order	0.012	0.004	0.016
ExpressionSet2subset	0.012	0.000	0.019
ExpressionSet2weightedSubset	0.296	0.004	0.340
RCMestimation	1.292	0.000	1.650
RCMrandom	1.400	0.008	1.699
RCMtest	5.004	0.016	5.998
cghCall2cghSeg	0.072	0.000	0.140
cghCall2maximumSubset	0.432	0.000	0.633
cghCall2order	0.028	0.000	0.028
cghCall2subset	0.068	0.000	0.070
cghCall2weightedSubset	0.332	0.004	0.336
cghSeg2order	0.068	0.004	0.074
cghSeg2subset	0.104	0.004	0.109
cghSeg2weightedSubset	0.312	0.000	0.412
cisEffectPlot	0.092	0.004	0.110
cisEffectTable	2.464	0.008	2.865
cisEffectTest	2.397	0.000	2.553
cisEffectTune	19.085	0.020	21.968
cisTest-class	0.000	0.004	0.002
entTest-class	0.000	0.000	0.001
entropyTest	0.236	0.000	0.246
expandMatching2singleIDs	0.056	0.000	0.057
getSegFeatures	0.012	0.000	0.024
hdEntropy	0.016	0.000	0.026
hdMI	0.480	0.000	0.555
matchAnn2Ann	0.040	0.000	0.042
matchCGHcall2ExpressionSet	0.076	0.000	0.203
merge2ExpressionSets	0.080	0.000	0.165
merge2cghCalls	0.116	0.000	0.220
miTest-class	0.000	0.000	0.001
mutInfTest	201.689	8.320	235.112
nBreakpoints	0.284	0.004	0.412
pathway1sample	0.200	0.020	0.356
pathway2sample	6.160	2.008	9.240
pathwayFit-class	0.000	0.000	0.001
pathwayPlot	0.160	0.004	0.439
pollackCN16	0.000	0.004	0.008
pollackGE16	0.000	0.000	0.003
profilesPlot	0.152	0.004	0.164
rcmFit-class	0	0	0
rcmTest-class	0.000	0.000	0.001
splitMatchingAtBreakpoints	0.316	0.000	0.370
uniqGenomicInfo	0.008	0.004	0.010