BioC 3.2: CHECK report for sigaR on zin1

Package: sigaR

Version: 1.13.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.13.0.tar.gz

StartedAt: 2015-08-24 03:47:21 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:50:31 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 190.3 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/sigaR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.13.0’
* 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 ... [3s/3s] 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’
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’
* 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 ... [141s/142s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mutInfTest    110.078  3.258 113.998
cisEffectTune  13.179  0.044  13.222
* 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
  ‘/home/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	0.786	0.020	0.806
ExpressionSet2order	0.009	0.000	0.009
ExpressionSet2subset	0.007	0.000	0.007
ExpressionSet2weightedSubset	0.158	0.004	0.161
RCMestimation	0.827	0.008	0.837
RCMrandom	0.734	0.000	0.734
RCMtest	2.945	0.000	2.942
cghCall2cghSeg	0.044	0.001	0.045
cghCall2maximumSubset	0.268	0.000	0.267
cghCall2order	0.012	0.000	0.013
cghCall2subset	0.046	0.000	0.045
cghCall2weightedSubset	0.203	0.000	0.203
cghSeg2order	0.046	0.000	0.049
cghSeg2subset	0.071	0.001	0.071
cghSeg2weightedSubset	0.183	0.000	0.183
cisEffectPlot	0.056	0.000	0.055
cisEffectTable	1.416	0.000	1.416
cisEffectTest	1.302	0.007	1.309
cisEffectTune	13.179	0.044	13.222
cisTest-class	0.001	0.000	0.002
entTest-class	0.001	0.000	0.000
entropyTest	0.135	0.004	0.139
expandMatching2singleIDs	0.034	0.000	0.034
getSegFeatures	0.008	0.000	0.008
hdEntropy	0.011	0.000	0.012
hdMI	0.272	0.000	0.272
matchAnn2Ann	0.03	0.00	0.03
matchCGHcall2ExpressionSet	0.038	0.004	0.042
merge2ExpressionSets	0.055	0.000	0.055
merge2cghCalls	0.07	0.00	0.07
miTest-class	0.001	0.000	0.001
mutInfTest	110.078	3.258	113.998
nBreakpoints	0.222	0.000	0.229
pathway1sample	0.111	0.000	0.111
pathway2sample	2.435	0.064	2.514
pathwayFit-class	0.001	0.000	0.001
pathwayPlot	0.097	0.000	0.097
pollackCN16	0.005	0.000	0.005
pollackGE16	0.002	0.000	0.002
profilesPlot	0.104	0.000	0.104
rcmFit-class	0.001	0.000	0.001
rcmTest-class	0.001	0.000	0.001
splitMatchingAtBreakpoints	0.159	0.000	0.178
uniqGenomicInfo	0.007	0.000	0.007