BioC 3.1: CHECK report for sigaR on zin2

Package: sigaR

Version: 1.12.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.12.0.tar.gz

StartedAt: 2015-10-09 05:30:15 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:33:08 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 172.5 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘1.12.0’
* 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 ... [128s/128s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
mutInfTest    99.465  2.922 102.505
cisEffectTune 12.197  0.004  12.197
* 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-3.1-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	0.718	0.004	0.721
ExpressionSet2order	0.008	0.000	0.008
ExpressionSet2subset	0.006	0.000	0.006
ExpressionSet2weightedSubset	0.141	0.004	0.145
RCMestimation	0.770	0.008	0.777
RCMrandom	0.714	0.000	0.715
RCMtest	2.847	0.004	2.848
cghCall2cghSeg	0.039	0.000	0.039
cghCall2maximumSubset	0.235	0.000	0.234
cghCall2order	0.012	0.000	0.012
cghCall2subset	0.042	0.000	0.042
cghCall2weightedSubset	0.181	0.000	0.180
cghSeg2order	0.04	0.00	0.04
cghSeg2subset	0.06	0.00	0.06
cghSeg2weightedSubset	0.164	0.000	0.164
cisEffectPlot	0.054	0.000	0.053
cisEffectTable	1.294	0.000	1.293
cisEffectTest	1.199	0.000	1.198
cisEffectTune	12.197	0.004	12.197
cisTest-class	0.001	0.000	0.001
entTest-class	0.001	0.000	0.001
entropyTest	0.123	0.000	0.123
expandMatching2singleIDs	0.03	0.00	0.03
getSegFeatures	0.007	0.000	0.007
hdEntropy	0.01	0.00	0.01
hdMI	0.25	0.00	0.25
matchAnn2Ann	0.026	0.000	0.026
matchCGHcall2ExpressionSet	0.100	0.000	0.101
merge2ExpressionSets	0.046	0.000	0.046
merge2cghCalls	0.064	0.000	0.064
miTest-class	0.001	0.000	0.000
mutInfTest	99.465	2.922	102.505
nBreakpoints	0.141	0.000	0.141
pathway1sample	0.099	0.004	0.103
pathway2sample	2.167	0.068	2.237
pathwayFit-class	0.001	0.000	0.001
pathwayPlot	0.086	0.000	0.086
pollackCN16	0.005	0.000	0.004
pollackGE16	0.002	0.000	0.002
profilesPlot	0.096	0.000	0.097
rcmFit-class	0.001	0.000	0.001
rcmTest-class	0.001	0.000	0.000
splitMatchingAtBreakpoints	0.139	0.000	0.139
uniqGenomicInfo	0.006	0.000	0.006