BioC 2.14: CHECK report for sigaR on petty

Package: sigaR

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sigaR_1.8.0.tar.gz

StartedAt: 2014-10-08 00:07:10 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:16:08 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 537.5 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 --no-multiarch sigaR_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/sigaR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.8.0’
* 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 ... [11s/15s] 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
cghCall2maximumSubset: no visible binding for global variable ‘sigaR’
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’
ExpressionSet2weightedSubset: no visible binding for global variable
  ‘sigaR’
matchAnn2Ann: no visible binding for global variable ‘sigaR’
matchCGHcall2ExpressionSet: no visible binding for global variable
  ‘sigaR’
mutInfTest: no visible binding for global variable ‘sigaR’
mutInfTest: no visible binding for global variable ‘corpcor’
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’
* 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 ... [362s/377s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     279.758 12.255 303.701
cisEffectTune   32.253  0.230  33.140
RCMtest          7.446  0.019   7.703
pathway2sample   5.220  1.302   6.711
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	2.188	0.047	2.283
ExpressionSet2order	0.021	0.001	0.029
ExpressionSet2subset	0.018	0.002	0.020
ExpressionSet2weightedSubset	0.355	0.011	0.375
RCMestimation	1.942	0.015	2.045
RCMrandom	2.205	0.006	2.305
RCMtest	7.446	0.019	7.703
cghCall2cghSeg	0.105	0.002	0.130
cghCall2maximumSubset	0.584	0.015	0.611
cghCall2order	0.034	0.002	0.040
cghCall2subset	0.103	0.001	0.108
cghCall2weightedSubset	0.541	0.004	0.552
cghSeg2order	0.100	0.001	0.102
cghSeg2subset	0.152	0.001	0.164
cghSeg2weightedSubset	0.409	0.003	0.429
cisEffectPlot	0.155	0.003	0.200
cisEffectTable	3.174	0.057	3.364
cisEffectTest	3.187	0.058	3.295
cisEffectTune	32.253	0.230	33.140
cisTest-class	0.003	0.001	0.004
entTest-class	0.002	0.000	0.002
entropyTest	0.276	0.002	0.288
expandMatching2singleIDs	0.082	0.002	0.087
getSegFeatures	0.015	0.001	0.015
hdEntropy	0.026	0.002	0.028
hdMI	0.511	0.004	0.534
matchAnn2Ann	0.067	0.002	0.322
matchCGHcall2ExpressionSet	0.104	0.002	0.107
merge2ExpressionSets	0.138	0.002	0.144
merge2cghCalls	0.184	0.001	0.189
miTest-class	0.002	0.000	0.002
mutInfTest	279.758	12.255	303.701
nBreakpoints	0.534	0.006	0.612
pathway1sample	0.245	0.015	0.271
pathway2sample	5.220	1.302	6.711
pathwayFit-class	0.003	0.000	0.002
pathwayPlot	0.202	0.005	0.208
pollackCN16	0.009	0.001	0.011
pollackGE16	0.005	0.001	0.032
profilesPlot	0.284	0.013	0.317
rcmFit-class	0.002	0.001	0.003
rcmTest-class	0.002	0.001	0.002
splitMatchingAtBreakpoints	0.513	0.004	0.530
uniqGenomicInfo	0.014	0.001	0.015