BioC 2.12: CHECK report for sigaR on petty

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: 2013-03-25 04:42:20 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:49:43 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 442.9 seconds

RetCode: 0

Status: WARNINGS

CheckDir: sigaR.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/sigaR.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 ... [9s/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 ... 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 ... [330s/334s] WARNING
Found the following significant warnings:

  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     217.185 59.526 280.392
cisEffectTune   23.973  0.105  24.081
pathway2sample   4.076  1.960   6.267
RCMtest          5.557  0.022   5.579
* 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

WARNING: There was 1 warning.
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
   'sigaR.Rnw' 
** testing if installed package can be loaded
* DONE (sigaR)

name	user	system	elapsed
CNGEheatmaps	1.235	0.068	1.308
ExpressionSet2order	0.020	0.005	0.025
ExpressionSet2subset	0.018	0.006	0.025
ExpressionSet2weightedSubset	0.243	0.017	0.260
RCMestimation	1.460	0.020	1.487
RCMrandom	1.465	0.018	1.484
RCMtest	5.557	0.022	5.579
cghCall2cghSeg	0.079	0.008	0.086
cghCall2maximumSubset	0.490	0.025	0.518
cghCall2order	0.097	0.010	0.109
cghCall2subset	0.08	0.01	0.09
cghCall2weightedSubset	0.323	0.021	0.345
cghSeg2order	0.091	0.012	0.104
cghSeg2subset	0.168	0.013	0.182
cghSeg2weightedSubset	0.366	0.018	0.384
cisEffectPlot	0.104	0.009	0.113
cisEffectTable	2.385	0.047	2.434
cisEffectTest	2.637	0.046	2.685
cisEffectTune	23.973	0.105	24.081
cisTest-class	0.010	0.006	0.016
entTest-class	0.006	0.005	0.011
entropyTest	0.175	0.013	0.189
expandMatching2singleIDs	0.076	0.015	0.091
getSegFeatures	0.020	0.008	0.028
hdEntropy	0.021	0.007	0.027
hdMI	0.304	0.008	0.312
matchAnn2Ann	0.067	0.014	0.081
matchCGHcall2ExpressionSet	0.082	0.010	0.094
merge2ExpressionSets	0.151	0.010	0.161
merge2cghCalls	0.120	0.012	0.133
miTest-class	0.006	0.006	0.012
mutInfTest	217.185	59.526	280.392
nBreakpoints	0.355	0.021	0.376
pathway1sample	0.197	0.052	0.253
pathway2sample	4.076	1.960	6.267
pathwayFit-class	0.004	0.006	0.009
pathwayPlot	0.153	0.049	0.213
pollackCN16	0.012	0.016	0.028
pollackGE16	0.005	0.005	0.009
profilesPlot	0.156	0.017	0.173
rcmFit-class	0.003	0.006	0.010
rcmTest-class	0.003	0.004	0.007
splitMatchingAtBreakpoints	0.307	0.019	0.326
uniqGenomicInfo	0.013	0.009	0.023

Summary

Command output