BioC 3.0: CHECK report for sigaR on perceval

Package: sigaR

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sigaR_1.10.0.tar.gz

StartedAt: 2015-04-10 06:23:11 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 06:31:38 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 507.6 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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/sigaR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.10.0’
* 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 ... [8s/10s] 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
.pi0est: no visible global function definition for ‘convest’
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’
ExpressionSet2weightedSubset: no visible binding for global variable
  ‘sigaR’
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’
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 ... [365s/399s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     297.565 15.250 343.682
cisEffectTune   21.653  0.229  21.926
pathway2sample   6.700  1.553  10.977
RCMtest          5.024  0.008   5.034
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	1.367	0.037	1.408
ExpressionSet2order	0.013	0.001	0.014
ExpressionSet2subset	0.010	0.001	0.012
ExpressionSet2weightedSubset	0.255	0.012	0.268
RCMestimation	1.331	0.012	1.345
RCMrandom	1.440	0.003	1.443
RCMtest	5.024	0.008	5.034
cghCall2cghSeg	0.064	0.000	0.064
cghCall2maximumSubset	0.509	0.021	0.531
cghCall2order	0.036	0.002	0.039
cghCall2subset	0.084	0.002	0.086
cghCall2weightedSubset	0.540	0.005	0.545
cghSeg2order	0.074	0.002	0.076
cghSeg2subset	0.130	0.002	0.142
cghSeg2weightedSubset	0.366	0.002	0.369
cisEffectPlot	0.103	0.003	0.116
cisEffectTable	2.599	0.074	2.674
cisEffectTest	2.238	0.060	2.299
cisEffectTune	21.653	0.229	21.926
cisTest-class	0.002	0.001	0.002
entTest-class	0.002	0.000	0.001
entropyTest	0.295	0.004	0.299
expandMatching2singleIDs	0.049	0.001	0.051
getSegFeatures	0.009	0.001	0.010
hdEntropy	0.014	0.001	0.015
hdMI	0.559	0.004	0.565
matchAnn2Ann	0.054	0.002	0.056
matchCGHcall2ExpressionSet	0.076	0.002	0.079
merge2ExpressionSets	0.085	0.002	0.099
merge2cghCalls	0.107	0.003	0.111
miTest-class	0.001	0.000	0.001
mutInfTest	297.565	15.250	343.682
nBreakpoints	0.311	0.005	0.378
pathway1sample	0.161	0.012	0.252
pathway2sample	6.700	1.553	10.977
pathwayFit-class	0.001	0.000	0.001
pathwayPlot	0.151	0.011	0.162
pollackCN16	0.006	0.002	0.007
pollackGE16	0.003	0.001	0.004
profilesPlot	0.157	0.059	0.221
rcmFit-class	0.001	0.000	0.002
rcmTest-class	0.002	0.000	0.002
splitMatchingAtBreakpoints	0.325	0.005	0.330
uniqGenomicInfo	0.008	0.001	0.009