BioC 3.0: CHECK report for sigaR on oaxaca

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 03:23:37 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:29:20 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 343.2 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

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


* 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-darwin13.4.0 (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 ... [6s/7s] 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’
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 ... [224s/257s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mutInfTest    177.985  7.071 217.405
cisEffectTune  17.279  0.156  17.725
* 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	1.193	0.025	1.221
ExpressionSet2order	0.014	0.000	0.015
ExpressionSet2subset	0.009	0.000	0.009
ExpressionSet2weightedSubset	0.209	0.007	0.217
RCMestimation	1.204	0.012	1.221
RCMrandom	1.266	0.010	1.280
RCMtest	4.379	0.015	4.419
cghCall2cghSeg	0.068	0.000	0.069
cghCall2maximumSubset	0.346	0.011	0.357
cghCall2order	0.020	0.000	0.021
cghCall2subset	0.066	0.000	0.067
cghCall2weightedSubset	0.352	0.008	0.361
cghSeg2order	0.070	0.001	0.070
cghSeg2subset	0.107	0.001	0.108
cghSeg2weightedSubset	0.243	0.003	0.247
cisEffectPlot	0.077	0.002	0.080
cisEffectTable	1.854	0.040	1.914
cisEffectTest	1.794	0.031	1.840
cisEffectTune	17.279	0.156	17.725
cisTest-class	0.001	0.000	0.002
entTest-class	0.001	0.000	0.002
entropyTest	0.167	0.002	0.168
expandMatching2singleIDs	0.042	0.001	0.043
getSegFeatures	0.009	0.001	0.009
hdEntropy	0.014	0.001	0.014
hdMI	0.307	0.002	0.309
matchAnn2Ann	0.037	0.002	0.038
matchCGHcall2ExpressionSet	0.057	0.001	0.059
merge2ExpressionSets	0.071	0.000	0.072
merge2cghCalls	0.093	0.002	0.094
miTest-class	0.001	0.000	0.001
mutInfTest	177.985	7.071	217.405
nBreakpoints	0.274	0.003	0.278
pathway1sample	0.139	0.005	0.144
pathway2sample	2.733	0.653	3.421
pathwayFit-class	0.001	0.000	0.001
pathwayPlot	0.116	0.006	0.121
pollackCN16	0.006	0.001	0.006
pollackGE16	0.003	0.001	0.004
profilesPlot	0.151	0.030	0.182
rcmFit-class	0.001	0.001	0.001
rcmTest-class	0.001	0.000	0.001
splitMatchingAtBreakpoints	0.281	0.003	0.284
uniqGenomicInfo	0.008	0.001	0.009