BioC 2.12: CHECK report for sigaR on george2

Package: sigaR

Version: 1.4.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.4.0.tar.gz

StartedAt: 2013-10-09 04:54:52 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 05:04:53 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 601.0 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/sigaR.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘1.4.0’
* 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 ... [10s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 for unstated 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 examples ... [454s/474s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     370.187 11.444 399.853
cisEffectTune   29.578  0.012  30.265
pathway2sample   9.953  0.964  11.338
RCMtest          6.949  0.004   7.184
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-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	1.908	0.044	1.953
ExpressionSet2order	0.040	0.000	0.039
ExpressionSet2subset	0.248	0.004	0.252
ExpressionSet2weightedSubset	0.352	0.012	0.365
RCMestimation	1.836	0.008	1.855
RCMrandom	2.040	0.000	2.099
RCMtest	6.949	0.004	7.184
cghCall2cghSeg	0.196	0.000	0.195
cghCall2maximumSubset	0.692	0.024	0.732
cghCall2order	0.312	0.000	0.311
cghCall2subset	0.096	0.004	0.099
cghCall2weightedSubset	0.572	0.008	0.579
cghSeg2order	0.128	0.000	0.131
cghSeg2subset	0.432	0.000	0.433
cghSeg2weightedSubset	0.564	0.012	0.579
cisEffectPlot	0.128	0.004	0.133
cisEffectTable	3.232	0.012	3.248
cisEffectTest	3.388	0.004	3.394
cisEffectTune	29.578	0.012	30.265
cisTest-class	0.016	0.004	0.020
entTest-class	0.024	0.004	0.031
entropyTest	0.480	0.004	0.493
expandMatching2singleIDs	0.136	0.004	0.142
getSegFeatures	0.052	0.000	0.052
hdEntropy	0.040	0.008	0.048
hdMI	0.768	0.000	0.768
matchAnn2Ann	0.076	0.008	0.084
matchCGHcall2ExpressionSet	0.116	0.000	0.114
merge2ExpressionSets	0.436	0.004	0.440
merge2cghCalls	0.200	0.000	0.202
miTest-class	0.02	0.00	0.02
mutInfTest	370.187	11.444	399.853
nBreakpoints	0.412	0.024	0.437
pathway1sample	0.320	0.020	0.344
pathway2sample	9.953	0.964	11.338
pathwayFit-class	0.008	0.000	0.007
pathwayPlot	0.232	0.020	0.255
pollackCN16	0.012	0.000	0.012
pollackGE16	0.020	0.000	0.019
profilesPlot	0.272	0.000	0.272
rcmFit-class	0.004	0.000	0.007
rcmTest-class	0.004	0.004	0.006
splitMatchingAtBreakpoints	0.400	0.008	0.412
uniqGenomicInfo	0.024	0.000	0.025