BioC 2.13: CHECK report for sigaR on zin1

Package: sigaR

Version: 1.6.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.6.0.tar.gz

StartedAt: 2014-04-05 03:57:26 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:01:23 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 236.6 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/sigaR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-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 ‘1.6.0’
* 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 ... [5s/5s] 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 installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘sigaR.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [171s/172s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mutInfTest    133.629  3.588 137.894
cisEffectTune  15.101  0.004  15.136
* 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 3 notes.
See
  ‘/home/biocbuild/bbs-2.13-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	1.076	0.024	1.106
ExpressionSet2order	0.016	0.000	0.016
ExpressionSet2subset	0.076	0.000	0.079
ExpressionSet2weightedSubset	0.180	0.020	0.204
RCMestimation	1.088	0.004	1.095
RCMrandom	1.116	0.000	1.322
RCMtest	4.008	0.036	4.079
cghCall2cghSeg	0.064	0.000	0.063
cghCall2maximumSubset	0.316	0.000	0.318
cghCall2order	0.020	0.004	0.023
cghCall2subset	0.060	0.000	0.061
cghCall2weightedSubset	0.308	0.000	0.308
cghSeg2order	0.064	0.000	0.063
cghSeg2subset	0.092	0.000	0.094
cghSeg2weightedSubset	0.220	0.000	0.219
cisEffectPlot	0.076	0.000	0.077
cisEffectTable	1.576	0.000	1.578
cisEffectTest	1.656	0.004	1.663
cisEffectTune	15.101	0.004	15.136
cisTest-class	0.004	0.000	0.003
entTest-class	0.004	0.000	0.003
entropyTest	0.148	0.000	0.148
expandMatching2singleIDs	0.052	0.000	0.049
getSegFeatures	0.004	0.004	0.011
hdEntropy	0.016	0.000	0.015
hdMI	0.272	0.000	0.275
matchAnn2Ann	0.036	0.004	0.040
matchCGHcall2ExpressionSet	0.056	0.000	0.057
merge2ExpressionSets	0.064	0.000	0.065
merge2cghCalls	0.088	0.000	0.087
miTest-class	0.004	0.000	0.004
mutInfTest	133.629	3.588	137.894
nBreakpoints	0.248	0.000	0.250
pathway1sample	0.140	0.004	0.146
pathway2sample	2.620	0.188	2.815
pathwayFit-class	0.000	0.000	0.002
pathwayPlot	0.108	0.000	0.107
pollackCN16	0.004	0.004	0.008
pollackGE16	0.000	0.004	0.003
profilesPlot	0.124	0.000	0.124
rcmFit-class	0.000	0.000	0.001
rcmTest-class	0.004	0.000	0.001
splitMatchingAtBreakpoints	0.22	0.00	0.22
uniqGenomicInfo	0.008	0.000	0.008