Package: sigaR

Version: 1.0.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings sigaR_1.0.0.tar.gz

StartedAt: 2012-04-01 03:23:32 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 03:26:49 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 196.3 seconds

RetCode: 0

Status:  OK

CheckDir: sigaR.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/sigaR.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sigaR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sigaR' version '1.0.0'
* 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 whether package 'sigaR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
CNGEheatmaps: warning in layout(matrix(c(1, 2, 3, 1, 2, 3, 1, 2, 3), 3,
  3, byrow = TRUE), width = c(1, 9, 9)): partial argument match of
  'width' to 'widths'
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'
entropyTest: no visible binding for global variable 'sigaR'
entropyTest: no visible binding for global variable 'corpcor'
hdEntropy : normEntropy: warning in round(lambda, d = 5): partial
  argument match of 'd' to 'digits'
hdMI : normMI: warning in round(lambda, d = 5): partial argument match
  of 'd' to 'digits'
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 ... OK
* 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
  '/loc/home/hpages/test-puck5/bbs-2.10-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	0.884	0.024	0.973
ExpressionSet2order	0.016	0.000	0.024
ExpressionSet2subset	0.008	0.000	0.017
ExpressionSet2weightedSubset	0.172	0.000	0.183
RCMestimation	1.148	0.000	1.169
RCMrandom	1.080	0.004	1.105
RCMtest	4.244	0.000	4.270
cghCall2maximumSubset	0.308	0.004	0.318
cghCall2order	0.020	0.000	0.026
cghCall2subset	0.052	0.000	0.059
cghCall2weightedSubset	0.224	0.000	0.234
entTest-class	0.000	0.004	0.000
entropyTest	0.140	0.000	0.149
expandMatching2singleIDs	0.048	0.000	0.062
getSegFeatures	0.008	0.000	0.018
hdEntropy	0.012	0.004	0.021
hdMI	0.248	0.000	0.263
matchAnn2Ann	0.040	0.000	0.054
matchCGHcall2ExpressionSet	0.056	0.000	0.073
merge2ExpressionSets	0.064	0.000	0.073
merge2cghCalls	0.084	0.000	0.097
miTest-class	0	0	0
mutInfTest	127.648	4.128	131.883
nBreakpoints	0.288	0.004	0.309
pollackCN16	0.000	0.004	0.015
pollackGE16	0.004	0.000	0.013
profilesPlot	0.152	0.008	0.176
rcmFit-class	0	0	0
rcmTest-class	0	0	0
splitMatchingAtBreakpoints	0.288	0.000	0.307
uniqGenomicInfo	0.012	0.000	0.024