BioC 3.2: CHECK report for sigaR on perceval

Package: sigaR

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sigaR_1.14.0.tar.gz

StartedAt: 2015-11-10 09:31:19 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 09:35:47 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 267.8 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sigaR_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/sigaR.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.14.0’
* 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 ... [5s/6s] 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
summary,entTest : .local: warning in round(object@statistic, d = 3):
  partial argument match of 'd' to 'digits'
summary,entTest : .local: warning in round(object@p.value, d = 3):
  partial argument match of 'd' to 'digits'
summary,miTest : .local: warning in round(object@statistic, d = 3):
  partial argument match of 'd' to 'digits'
summary,miTest : .local: warning in round(object@p.value, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmFit : .local: warning in round(object@betas, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmFit : .local: warning in round(object@tau2s, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmFit : .local: warning in round(object@av.sigma2s, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmFit : .local: warning in round(object@rho, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmFit : .local: warning in round(object@shrinkage, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmFit : .local: warning in round(object@loglik, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@betas, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@tau2s, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@av.sigma2s, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@rho, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@shrinkage, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@loglik, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@statistic, d = 3):
  partial argument match of 'd' to 'digits'
summary,rcmTest : .local: warning in round(object@p.value, d = 3):
  partial argument match of 'd' to 'digits'
.pi0est: no visible global function definition for ‘convest’
cghCall2maximumSubset: no visible binding for global variable ‘sigaR’
cghCall2order: no visible global function definition for ‘probdloss’
cghCall2order: no visible global function definition for ‘probdloss<-’
cghCall2subset: no visible global function definition for ‘probdloss’
cghCall2weightedSubset: no visible global function definition for
  ‘probdloss’
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’
merge2cghCalls: no visible global function definition for ‘probdloss’
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 files in ‘vignettes’ ... OK
* checking examples ... [196s/196s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mutInfTest    146.383 10.131 156.524
cisEffectTune  18.239  0.175  18.415
* 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
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	1.114	0.018	1.133
ExpressionSet2order	0.011	0.000	0.012
ExpressionSet2subset	0.008	0.000	0.009
ExpressionSet2weightedSubset	0.201	0.008	0.210
RCMestimation	1.109	0.011	1.121
RCMrandom	1.028	0.001	1.030
RCMtest	4.069	0.003	4.072
cghCall2cghSeg	0.058	0.000	0.058
cghCall2maximumSubset	0.345	0.004	0.349
cghCall2order	0.017	0.000	0.017
cghCall2subset	0.056	0.000	0.056
cghCall2weightedSubset	0.256	0.002	0.259
cghSeg2order	0.057	0.001	0.058
cghSeg2subset	0.090	0.001	0.091
cghSeg2weightedSubset	0.242	0.003	0.245
cisEffectPlot	0.074	0.003	0.075
cisEffectTable	1.909	0.045	1.954
cisEffectTest	1.823	0.050	1.872
cisEffectTune	18.239	0.175	18.415
cisTest-class	0.002	0.001	0.002
entTest-class	0.001	0.000	0.001
entropyTest	0.171	0.002	0.173
expandMatching2singleIDs	0.041	0.001	0.042
getSegFeatures	0.008	0.001	0.009
hdEntropy	0.012	0.001	0.012
hdMI	0.340	0.002	0.342
matchAnn2Ann	0.034	0.001	0.035
matchCGHcall2ExpressionSet	0.051	0.002	0.053
merge2ExpressionSets	0.061	0.001	0.062
merge2cghCalls	0.087	0.002	0.089
miTest-class	0.001	0.000	0.002
mutInfTest	146.383	10.131	156.524
nBreakpoints	0.218	0.003	0.222
pathway1sample	0.128	0.008	0.136
pathway2sample	3.129	0.935	4.064
pathwayFit-class	0.001	0.000	0.001
pathwayPlot	0.115	0.007	0.122
pollackCN16	0.005	0.001	0.007
pollackGE16	0.003	0.001	0.003
profilesPlot	0.131	0.035	0.166
rcmFit-class	0.001	0.000	0.002
rcmTest-class	0.002	0.000	0.002
splitMatchingAtBreakpoints	0.213	0.002	0.216
uniqGenomicInfo	0.007	0.001	0.007