BioC 3.2: CHECK report for sigaR on zin1

Package: sigaR

Version: 1.14.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.14.0.tar.gz

StartedAt: 2016-04-23 05:25:35 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 05:29:37 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 242.3 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_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/sigaR.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.14.0’
* 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 ... [6s/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’
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 ... [170s/172s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mutInfTest    138.702  2.403 142.371
cisEffectTune  12.396  0.000  12.396
* 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	0.960	0.008	0.980
ExpressionSet2order	0.008	0.000	0.009
ExpressionSet2subset	0.007	0.000	0.006
ExpressionSet2weightedSubset	0.213	0.000	0.215
RCMestimation	0.719	0.004	0.742
RCMrandom	0.795	0.000	0.795
RCMtest	2.925	0.000	2.923
cghCall2cghSeg	0.045	0.000	0.045
cghCall2maximumSubset	0.335	0.008	0.343
cghCall2order	0.012	0.000	0.013
cghCall2subset	0.041	0.000	0.041
cghCall2weightedSubset	0.271	0.004	0.274
cghSeg2order	0.047	0.000	0.047
cghSeg2subset	0.067	0.000	0.067
cghSeg2weightedSubset	0.239	0.000	0.239
cisEffectPlot	0.055	0.000	0.055
cisEffectTable	1.316	0.004	1.319
cisEffectTest	1.268	0.000	1.267
cisEffectTune	12.396	0.000	12.396
cisTest-class	0.001	0.000	0.001
entTest-class	0.001	0.000	0.001
entropyTest	0.204	0.000	0.203
expandMatching2singleIDs	0.031	0.000	0.032
getSegFeatures	0.003	0.004	0.007
hdEntropy	0.006	0.004	0.010
hdMI	0.466	0.000	0.467
matchAnn2Ann	0.03	0.00	0.03
matchCGHcall2ExpressionSet	0.041	0.000	0.041
merge2ExpressionSets	0.046	0.004	0.050
merge2cghCalls	0.072	0.000	0.072
miTest-class	0.000	0.000	0.001
mutInfTest	138.702	2.403	142.371
nBreakpoints	0.132	0.004	0.137
pathway1sample	0.102	0.008	0.110
pathway2sample	3.073	0.084	3.168
pathwayFit-class	0.001	0.000	0.001
pathwayPlot	0.093	0.000	0.093
pollackCN16	0.005	0.000	0.006
pollackGE16	0.003	0.000	0.003
profilesPlot	0.102	0.000	0.101
rcmFit-class	0.001	0.000	0.001
rcmTest-class	0.001	0.000	0.001
splitMatchingAtBreakpoints	0.162	0.000	0.162
uniqGenomicInfo	0.007	0.000	0.007