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: 2015-10-22 11:20:15 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 11:23:21 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 185.9 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 Under development (unstable) (2015-10-08 r69496)
* 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 ... [4s/4s] 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'
.pi0est: no visible global function definition for ‘convest’
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’
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’
Undefined global functions or variables:
  MASS convest corpcor probdloss probdloss<- quadprog sigaR
* 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 ... [122s/123s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
mutInfTest    90.775  6.298  98.571
cisEffectTune 11.142  0.126  11.321
* 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	0.715	0.015	0.732
ExpressionSet2order	0.006	0.000	0.007
ExpressionSet2subset	0.005	0.001	0.005
ExpressionSet2weightedSubset	0.119	0.004	0.123
RCMestimation	0.703	0.020	0.725
RCMrandom	0.731	0.009	0.741
RCMtest	2.758	0.009	2.770
cghCall2cghSeg	0.040	0.000	0.041
cghCall2maximumSubset	0.198	0.005	0.203
cghCall2order	0.014	0.001	0.014
cghCall2subset	0.047	0.000	0.049
cghCall2weightedSubset	0.171	0.001	0.172
cghSeg2order	0.046	0.001	0.047
cghSeg2subset	0.055	0.000	0.056
cghSeg2weightedSubset	0.162	0.006	0.168
cisEffectPlot	0.071	0.003	0.074
cisEffectTable	1.130	0.027	1.156
cisEffectTest	0.989	0.024	1.014
cisEffectTune	11.142	0.126	11.321
cisTest-class	0.001	0.000	0.001
entTest-class	0.001	0.000	0.001
entropyTest	0.101	0.004	0.106
expandMatching2singleIDs	0.024	0.001	0.025
getSegFeatures	0.006	0.000	0.007
hdEntropy	0.010	0.000	0.011
hdMI	0.218	0.003	0.221
matchAnn2Ann	0.020	0.001	0.021
matchCGHcall2ExpressionSet	0.031	0.001	0.032
merge2ExpressionSets	0.036	0.000	0.037
merge2cghCalls	0.055	0.002	0.057
miTest-class	0.001	0.000	0.000
mutInfTest	90.775	6.298	98.571
nBreakpoints	0.122	0.002	0.125
pathway1sample	0.078	0.005	0.082
pathway2sample	2.169	0.592	2.867
pathwayFit-class	0.001	0.000	0.001
pathwayPlot	0.068	0.016	0.084
pollackCN16	0.003	0.000	0.003
pollackGE16	0.002	0.000	0.003
profilesPlot	0.081	0.005	0.086
rcmFit-class	0.001	0.000	0.001
rcmTest-class	0.000	0.000	0.001
splitMatchingAtBreakpoints	0.133	0.002	0.135
uniqGenomicInfo	0.005	0.000	0.005