BioC 2.14: CHECK report for sigaR on morelia

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 01:33:25 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:38:21 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 296.6 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-darwin13.1.0 (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 ... [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
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’
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’
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 ... [212s/212s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mutInfTest    167.989  6.654 174.929
cisEffectTune  16.606  0.117  16.737
* 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	1.230	0.024	1.256
ExpressionSet2order	0.010	0.001	0.011
ExpressionSet2subset	0.009	0.000	0.010
ExpressionSet2weightedSubset	0.204	0.005	0.210
RCMestimation	1.106	0.011	1.118
RCMrandom	1.218	0.007	1.227
RCMtest	4.054	0.014	4.070
cghCall2cghSeg	0.057	0.001	0.057
cghCall2maximumSubset	0.314	0.010	0.324
cghCall2order	0.023	0.001	0.024
cghCall2subset	0.058	0.001	0.059
cghCall2weightedSubset	0.326	0.007	0.333
cghSeg2order	0.064	0.001	0.065
cghSeg2subset	0.113	0.001	0.114
cghSeg2weightedSubset	0.253	0.003	0.256
cisEffectPlot	0.102	0.002	0.104
cisEffectTable	1.814	0.024	1.841
cisEffectTest	1.767	0.031	1.799
cisEffectTune	16.606	0.117	16.737
cisTest-class	0.002	0.000	0.002
entTest-class	0.001	0.000	0.001
entropyTest	0.179	0.003	0.181
expandMatching2singleIDs	0.041	0.001	0.042
getSegFeatures	0.009	0.001	0.009
hdEntropy	0.018	0.002	0.019
hdMI	0.311	0.002	0.313
matchAnn2Ann	0.041	0.001	0.042
matchCGHcall2ExpressionSet	0.058	0.001	0.059
merge2ExpressionSets	0.075	0.001	0.077
merge2cghCalls	0.108	0.001	0.110
miTest-class	0.001	0.000	0.002
mutInfTest	167.989	6.654	174.929
nBreakpoints	0.266	0.002	0.269
pathway1sample	0.129	0.011	0.141
pathway2sample	2.773	0.662	3.439
pathwayFit-class	0.000	0.000	0.001
pathwayPlot	0.110	0.002	0.111
pollackCN16	0.005	0.000	0.007
pollackGE16	0.003	0.001	0.004
profilesPlot	0.167	0.031	0.198
rcmFit-class	0.001	0.001	0.001
rcmTest-class	0.001	0.000	0.002
splitMatchingAtBreakpoints	0.304	0.004	0.309
uniqGenomicInfo	0.008	0.001	0.009