Package: sigaR

Version: 1.3.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.3.1.tar.gz

StartedAt: 2013-01-16 06:19:11 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 06:25:47 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 396.5 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/sigaR.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.3.1’
* 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 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     245.324  7.176 256.295
cisEffectTune   21.841  0.004  21.849
pathway2sample   6.188  0.452   6.643
RCMtest          5.408  0.004   5.413
* 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-2.12-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
   ‘sigaR.Rnw’ 
** testing if installed package can be loaded

* DONE (sigaR)

name	user	system	elapsed
CNGEheatmaps	1.472	0.024	1.499
ExpressionSet2order	0.024	0.000	0.025
ExpressionSet2subset	0.148	0.000	0.147
ExpressionSet2weightedSubset	0.304	0.004	0.312
RCMestimation	1.384	0.004	1.394
RCMrandom	1.416	0.000	1.417
RCMtest	5.408	0.004	5.413
cghCall2cghSeg	0.088	0.004	0.092
cghCall2maximumSubset	0.516	0.008	0.526
cghCall2order	0.036	0.000	0.037
cghCall2subset	0.076	0.000	0.074
cghCall2weightedSubset	0.360	0.000	0.367
cghSeg2order	0.092	0.000	0.092
cghSeg2subset	0.252	0.000	0.256
cghSeg2weightedSubset	0.332	0.000	0.335
cisEffectPlot	0.108	0.000	0.106
cisEffectTable	2.445	0.000	2.444
cisEffectTest	2.428	0.004	2.436
cisEffectTune	21.841	0.004	21.849
cisTest-class	0.008	0.004	0.012
entTest-class	0.012	0.000	0.012
entropyTest	0.300	0.008	0.305
expandMatching2singleIDs	0.068	0.008	0.078
getSegFeatures	0.156	0.004	0.159
hdEntropy	0.024	0.000	0.022
hdMI	0.500	0.004	0.505
matchAnn2Ann	0.072	0.000	0.069
matchCGHcall2ExpressionSet	0.080	0.000	0.084
merge2ExpressionSets	0.092	0.000	0.092
merge2cghCalls	0.120	0.004	0.126
miTest-class	0.012	0.000	0.012
mutInfTest	245.324	7.176	256.295
nBreakpoints	0.312	0.016	0.326
pathway1sample	0.228	0.004	0.231
pathway2sample	6.188	0.452	6.643
pathwayFit-class	0.004	0.000	0.004
pathwayPlot	0.188	0.000	0.189
pollackCN16	0.004	0.004	0.008
pollackGE16	0.008	0.000	0.007
profilesPlot	0.164	0.004	0.169
rcmFit-class	0.008	0.000	0.004
rcmTest-class	0.000	0.004	0.004
splitMatchingAtBreakpoints	0.324	0.004	0.331
uniqGenomicInfo	0.012	0.000	0.015