BioC 3.3: CHECK report for sigaR on morelia

Package: sigaR

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings sigaR_1.15.0.tar.gz

StartedAt: 2016-04-21 07:34:20 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 07:38:32 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 252.2 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_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/sigaR.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.15.0’
* 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 ... [7s/7s] 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: warning in round(object@statistic, d = 3): partial
  argument match of 'd' to 'digits'
summary,entTest: warning in round(object@p.value, d = 3): partial
  argument match of 'd' to 'digits'
summary,miTest: warning in round(object@statistic, d = 3): partial
  argument match of 'd' to 'digits'
summary,miTest: warning in round(object@p.value, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmFit: warning in round(object@betas, d = 3): partial argument
  match of 'd' to 'digits'
summary,rcmFit: warning in round(object@tau2s, d = 3): partial argument
  match of 'd' to 'digits'
summary,rcmFit: warning in round(object@av.sigma2s, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmFit: warning in round(object@rho, d = 3): partial argument
  match of 'd' to 'digits'
summary,rcmFit: warning in round(object@shrinkage, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmFit: warning in round(object@loglik, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmTest: warning in round(object@betas, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmTest: warning in round(object@tau2s, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmTest: warning in round(object@av.sigma2s, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmTest: warning in round(object@rho, d = 3): partial argument
  match of 'd' to 'digits'
summary,rcmTest: warning in round(object@shrinkage, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmTest: warning in round(object@loglik, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmTest: warning in round(object@statistic, d = 3): partial
  argument match of 'd' to 'digits'
summary,rcmTest: warning in round(object@p.value, d = 3): partial
  argument match of 'd' to 'digits'
.R2.stat: no visible binding for global variable ‘var’
.countdiscoveries: no visible global function definition for ‘p.adjust’
.lambda.per.reg: no visible global function definition for ‘cor’
.pi0est: no visible global function definition for ‘convest’
.shrin.an.prob: no visible global function definition for ‘p.adjust’
.shrin.an.wcvm: no visible global function definition for ‘p.adjust’
.uni.an.prob: no visible global function definition for ‘p.adjust’
.uni.an.wcvm: no visible global function definition for ‘p.adjust’
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’
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’
cisEffectPlot: no visible global function definition for ‘symbols’
cisEffectTest: no visible global function definition for ‘p.adjust’
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’
merge2cghCalls: no visible global function definition for ‘probdloss’
mutInfTest: no visible binding for global variable ‘sigaR’
mutInfTest: no visible binding for global variable ‘corpcor’
pathway1sample: no visible global function definition for ‘coef’
pathway1sample: no visible global function definition for ‘var’
pathway1sample: no visible global function definition for ‘residuals’
pathway2sample: no visible global function definition for ‘coef’
pathway2sample: no visible global function definition for ‘var’
pathwayPlot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  MASS coef convest cor corpcor legend p.adjust probdloss probdloss<-
  quadprog residuals sigaR symbols var
Consider adding
  importFrom("graphics", "legend", "symbols")
  importFrom("stats", "coef", "cor", "p.adjust", "residuals", "var")
to your NAMESPACE file.
* 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 ... [171s/172s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mutInfTest    129.366  8.070 137.594
cisEffectTune  15.322  0.243  15.582
* 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-3.3-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	1.102	0.027	1.130
ExpressionSet2order	0.012	0.001	0.013
ExpressionSet2subset	0.009	0.002	0.011
ExpressionSet2weightedSubset	0.227	0.002	0.231
RCMestimation	0.810	0.025	0.837
RCMrandom	0.765	0.010	0.776
RCMtest	3.119	0.007	3.128
cghCall2cghSeg	0.034	0.000	0.035
cghCall2maximumSubset	0.359	0.005	0.364
cghCall2order	0.012	0.000	0.013
cghCall2subset	0.048	0.002	0.049
cghCall2weightedSubset	0.293	0.002	0.297
cghSeg2order	0.056	0.001	0.057
cghSeg2subset	0.066	0.002	0.068
cghSeg2weightedSubset	0.253	0.001	0.254
cisEffectPlot	0.048	0.003	0.052
cisEffectTable	1.456	0.050	1.507
cisEffectTest	1.658	0.041	1.703
cisEffectTune	15.322	0.243	15.582
cisTest-class	0.002	0.001	0.003
entTest-class	0.001	0.000	0.002
entropyTest	0.207	0.004	0.212
expandMatching2singleIDs	0.037	0.002	0.039
getSegFeatures	0.008	0.001	0.009
hdEntropy	0.012	0.002	0.012
hdMI	0.480	0.003	0.483
matchAnn2Ann	0.029	0.003	0.032
matchCGHcall2ExpressionSet	0.045	0.003	0.047
merge2ExpressionSets	0.049	0.001	0.050
merge2cghCalls	0.075	0.003	0.078
miTest-class	0.001	0.001	0.002
mutInfTest	129.366	8.070	137.594
nBreakpoints	0.164	0.004	0.169
pathway1sample	0.112	0.013	0.125
pathway2sample	2.963	0.634	3.601
pathwayFit-class	0.002	0.000	0.001
pathwayPlot	0.099	0.021	0.121
pollackCN16	0.005	0.001	0.006
pollackGE16	0.003	0.001	0.005
profilesPlot	0.111	0.004	0.115
rcmFit-class	0.001	0.000	0.001
rcmTest-class	0.002	0.001	0.002
splitMatchingAtBreakpoints	0.173	0.005	0.179
uniqGenomicInfo	0.006	0.002	0.007