Package: phenoDist

Version: 1.7.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings phenoDist_1.7.0.tar.gz

StartedAt: 2013-01-16 05:11:20 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 05:19:55 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 515.2 seconds

RetCode: 0

Status:  OK

CheckDir: phenoDist.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/phenoDist.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phenoDist/DESCRIPTION’ ... OK
* this is package ‘phenoDist’ version ‘1.7.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘phenoDist’ can be installed ... 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
distToNeg            176.459  0.072 176.597
PDMBySvmWeightVector  22.357  0.080  22.444
PDMBySvmAccuracy      11.785  0.040  11.827
PDMByKS               10.593  0.132  59.868
PDMByFactorAnalysis    4.520  0.100  21.979
* 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/biocbuild/bbs-2.12-bioc/meat/phenoDist.Rcheck/00check.log’
for details.

* installing *source* package ‘phenoDist’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘phenoDist.Rnw’ 
** testing if installed package can be loaded

* DONE (phenoDist)

name	user	system	elapsed
PDMByFactorAnalysis	4.520	0.100	21.979
PDMByKS	10.593	0.132	59.868
PDMBySvmAccuracy	11.785	0.040	11.827
PDMBySvmWeightVector	22.357	0.080	22.444
PDMByWellAvg	1.796	0.012	4.306
clusterDist	1.160	0.024	1.186
ctlSeparatn	0.008	0.000	0.010
distToNeg	176.459	0.072	176.597
enrichAnalysis	0.004	0.000	0.003
repCorr	0.012	0.000	0.012
repDistRank	0.012	0.000	0.012