Package: sigaR

Version: 1.3.2

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.3.2.tar.gz

StartedAt: 2013-03-25 04:36:57 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:47:13 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 615.1 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 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.3.2’
* 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 ... 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 ... [473s/484s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
mutInfTest     388.832 11.076 408.953
cisEffectTune   29.542  0.028  29.787
pathway2sample  10.576  0.700  11.525
RCMtest          6.957  0.012   7.245
* 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
  ‘/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
   ‘sigaR.Rnw’ 
** testing if installed package can be loaded
* DONE (sigaR)

name	user	system	elapsed
CNGEheatmaps	2.304	0.152	2.916
ExpressionSet2order	0.028	0.004	0.032
ExpressionSet2subset	0.028	0.000	0.024
ExpressionSet2weightedSubset	0.428	0.008	0.493
RCMestimation	1.812	0.004	1.894
RCMrandom	1.900	0.024	2.160
RCMtest	6.957	0.012	7.245
cghCall2cghSeg	0.136	0.000	0.137
cghCall2maximumSubset	0.636	0.004	0.642
cghCall2order	0.052	0.004	0.052
cghCall2subset	0.112	0.000	0.113
cghCall2weightedSubset	0.740	0.000	0.745
cghSeg2order	0.148	0.004	0.148
cghSeg2subset	0.172	0.000	0.172
cghSeg2weightedSubset	0.496	0.000	0.502
cisEffectPlot	0.144	0.000	0.143
cisEffectTable	3.228	0.008	3.239
cisEffectTest	3.072	0.004	3.118
cisEffectTune	29.542	0.028	29.787
cisTest-class	0.024	0.000	0.025
entTest-class	0.016	0.000	0.017
entropyTest	0.424	0.004	0.492
expandMatching2singleIDs	0.112	0.000	0.115
getSegFeatures	0.228	0.012	0.239
hdEntropy	0.032	0.004	0.035
hdMI	0.912	0.004	0.923
matchAnn2Ann	0.088	0.004	0.103
matchCGHcall2ExpressionSet	0.144	0.004	0.152
merge2ExpressionSets	0.124	0.000	0.198
merge2cghCalls	0.160	0.000	0.158
miTest-class	0.008	0.000	0.010
mutInfTest	388.832	11.076	408.953
nBreakpoints	0.432	0.032	0.466
pathway1sample	0.321	0.024	0.345
pathway2sample	10.576	0.700	11.525
pathwayFit-class	0.008	0.000	0.009
pathwayPlot	0.332	0.000	0.332
pollackCN16	0.012	0.000	0.012
pollackGE16	0.020	0.008	0.027
profilesPlot	0.356	0.000	0.355
rcmFit-class	0.012	0.000	0.014
rcmTest-class	0.012	0.000	0.010
splitMatchingAtBreakpoints	0.576	0.000	0.573
uniqGenomicInfo	0.024	0.000	0.026