BioC 2.13: CHECK report for sigaR on perceval

Package: sigaR

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sigaR_1.6.0.tar.gz

StartedAt: 2014-04-05 04:19:52 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:27:48 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 476.0 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/sigaR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.6.0’
* 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 ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘mvtnorm’ ‘penalized’
A package should be listed in only one of these fields.
* 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 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
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’
ExpressionSet2weightedSubset: no visible binding for global variable
  ‘sigaR’
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’
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’
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘sigaR.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [352s/362s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     271.586 21.828 298.975
cisEffectTune   23.878  0.342  26.511
pathway2sample   7.395  1.425   8.942
RCMtest          5.373  0.024   5.800
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	1.755	0.054	1.829
ExpressionSet2order	0.024	0.002	0.025
ExpressionSet2subset	0.023	0.001	0.024
ExpressionSet2weightedSubset	0.313	0.013	0.326
RCMestimation	1.382	0.008	1.412
RCMrandom	1.561	0.007	1.584
RCMtest	5.373	0.024	5.800
cghCall2cghSeg	0.081	0.001	0.090
cghCall2maximumSubset	0.511	0.017	0.591
cghCall2order	0.031	0.001	0.032
cghCall2subset	0.094	0.003	0.108
cghCall2weightedSubset	0.402	0.006	0.435
cghSeg2order	0.090	0.002	0.114
cghSeg2subset	0.142	0.002	0.155
cghSeg2weightedSubset	0.389	0.003	0.420
cisEffectPlot	0.120	0.004	0.135
cisEffectTable	2.760	0.092	3.272
cisEffectTest	2.539	0.087	2.932
cisEffectTune	23.878	0.342	26.511
cisTest-class	0.010	0.000	0.013
entTest-class	0.011	0.001	0.011
entropyTest	0.298	0.004	0.326
expandMatching2singleIDs	0.094	0.007	0.158
getSegFeatures	0.027	0.002	0.048
hdEntropy	0.032	0.001	0.034
hdMI	0.598	0.006	0.650
matchAnn2Ann	0.070	0.004	0.102
matchCGHcall2ExpressionSet	0.091	0.002	0.101
merge2ExpressionSets	0.112	0.002	0.121
merge2cghCalls	0.138	0.005	0.191
miTest-class	0.009	0.001	0.010
mutInfTest	271.586	21.828	298.975
nBreakpoints	0.377	0.022	0.402
pathway1sample	0.254	0.040	0.301
pathway2sample	7.395	1.425	8.942
pathwayFit-class	0.003	0.004	0.008
pathwayPlot	0.152	0.025	0.180
pollackCN16	0.007	0.005	0.012
pollackGE16	0.012	0.012	0.025
profilesPlot	0.186	0.012	0.199
rcmFit-class	0.003	0.004	0.007
rcmTest-class	0.004	0.005	0.010
splitMatchingAtBreakpoints	0.337	0.019	0.360
uniqGenomicInfo	0.012	0.007	0.020