BioC 2.12: CHECK report for sigaR on petty

Package: sigaR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sigaR_1.4.0.tar.gz

StartedAt: 2013-10-08 23:54:42 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-09 00:03:12 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 510.0 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/sigaR.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* 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 ... [11s/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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [368s/374s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     275.077 17.709 297.161
cisEffectTune   34.817  0.308  35.546
RCMtest          8.295  0.029   8.407
pathway2sample   5.472  1.302   6.824
* 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
  '/Users/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	2.200	0.052	2.285
ExpressionSet2order	0.032	0.002	0.033
ExpressionSet2subset	0.027	0.002	0.031
ExpressionSet2weightedSubset	0.374	0.014	0.389
RCMestimation	2.219	0.061	2.292
RCMrandom	2.300	0.013	2.323
RCMtest	8.295	0.029	8.407
cghCall2cghSeg	0.121	0.001	0.122
cghCall2maximumSubset	0.637	0.016	0.656
cghCall2order	0.053	0.002	0.055
cghCall2subset	0.110	0.002	0.112
cghCall2weightedSubset	0.479	0.007	0.490
cghSeg2order	0.120	0.001	0.122
cghSeg2subset	0.317	0.001	0.320
cghSeg2weightedSubset	0.476	0.012	0.492
cisEffectPlot	0.167	0.004	0.174
cisEffectTable	3.420	0.062	3.667
cisEffectTest	3.110	0.059	3.178
cisEffectTune	34.817	0.308	35.546
cisTest-class	0.013	0.001	0.014
entTest-class	0.010	0.000	0.011
entropyTest	0.320	0.004	0.330
expandMatching2singleIDs	0.112	0.005	0.117
getSegFeatures	0.029	0.001	0.030
hdEntropy	0.165	0.002	0.168
hdMI	0.541	0.005	0.560
matchAnn2Ann	0.086	0.005	0.093
matchCGHcall2ExpressionSet	0.126	0.002	0.135
merge2ExpressionSets	0.138	0.004	0.151
merge2cghCalls	0.188	0.002	0.201
miTest-class	0.008	0.000	0.009
mutInfTest	275.077	17.709	297.161
nBreakpoints	0.523	0.017	0.554
pathway1sample	0.286	0.030	0.323
pathway2sample	5.472	1.302	6.824
pathwayFit-class	0.003	0.005	0.008
pathwayPlot	0.231	0.066	0.323
pollackCN16	0.010	0.005	0.015
pollackGE16	0.007	0.004	0.011
profilesPlot	0.277	0.018	0.314
rcmFit-class	0.003	0.005	0.007
rcmTest-class	0.003	0.004	0.009
splitMatchingAtBreakpoints	0.534	0.021	0.577
uniqGenomicInfo	0.017	0.007	0.026