BioC 2.12: CHECK report for sigaR on pelham

Package: sigaR

Version: 1.3.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch sigaR_1.3.2.tar.gz

StartedAt: 2013-03-24 10:13:35 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 10:22:13 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 517.6 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 3.0.0 beta (2013-03-21 r62346)
* 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 '1.3.2'
* 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/10s] 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 ... NOTE
  '.find.package' is deprecated.
  Use 'find.package' instead.
  See help("Deprecated")
  '.find.package' is deprecated.
  Use 'find.package' instead.
  See help("Deprecated")
  '.find.package' is deprecated.
  Use 'find.package' instead.
  See help("Deprecated")
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [392s/399s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     293.842 32.713 332.716
cisEffectTune   28.348  0.306  29.005
pathway2sample   6.187  1.413   7.766
RCMtest          6.839  0.050   6.938
* 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 were 2 notes.
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
   'sigaR.Rnw' 
** testing if installed package can be loaded
* DONE (sigaR)

name	user	system	elapsed
CNGEheatmaps	1.811	0.044	1.856
ExpressionSet2order	0.032	0.002	0.033
ExpressionSet2subset	0.165	0.002	0.168
ExpressionSet2weightedSubset	0.353	0.020	0.375
RCMestimation	1.868	0.017	1.895
RCMrandom	1.965	0.012	1.987
RCMtest	6.839	0.050	6.938
cghCall2cghSeg	0.102	0.002	0.104
cghCall2maximumSubset	0.565	0.023	0.588
cghCall2order	0.043	0.002	0.045
cghCall2subset	0.099	0.002	0.102
cghCall2weightedSubset	0.458	0.014	0.472
cghSeg2order	0.118	0.002	0.120
cghSeg2subset	0.294	0.004	0.297
cghSeg2weightedSubset	0.398	0.004	0.403
cisEffectPlot	0.165	0.008	0.175
cisEffectTable	3.048	0.080	3.129
cisEffectTest	2.846	0.078	2.969
cisEffectTune	28.348	0.306	29.005
cisTest-class	0.014	0.002	0.016
entTest-class	0.008	0.001	0.009
entropyTest	0.268	0.003	0.273
expandMatching2singleIDs	0.090	0.005	0.095
getSegFeatures	0.028	0.004	0.032
hdEntropy	0.026	0.002	0.028
hdMI	0.498	0.006	0.506
matchAnn2Ann	0.078	0.006	0.087
matchCGHcall2ExpressionSet	0.230	0.004	0.234
merge2ExpressionSets	0.105	0.003	0.109
merge2cghCalls	0.149	0.003	0.153
miTest-class	0.011	0.001	0.012
mutInfTest	293.842	32.713	332.716
nBreakpoints	0.420	0.018	0.446
pathway1sample	0.265	0.035	0.307
pathway2sample	6.187	1.413	7.766
pathwayFit-class	0.003	0.005	0.009
pathwayPlot	0.193	0.031	0.242
pollackCN16	0.009	0.007	0.017
pollackGE16	0.013	0.021	0.034
profilesPlot	0.201	0.016	0.220
rcmFit-class	0.003	0.005	0.008
rcmTest-class	0.004	0.006	0.009
splitMatchingAtBreakpoints	0.399	0.031	0.445
uniqGenomicInfo	0.016	0.009	0.026

Summary

Command output