Package: BioSeqClass

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BioSeqClass_1.14.0.tar.gz

StartedAt: 2012-09-23 23:28:07 -0700 (Sun, 23 Sep 2012)

EndedAt: 2012-09-23 23:32:10 -0700 (Sun, 23 Sep 2012)

EllapsedTime: 243.3 seconds

RetCode: 0

Status:  OK

CheckDir: BioSeqClass.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/BioSeqClass.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BioSeqClass/DESCRIPTION' ... OK
* this is package 'BioSeqClass' version '1.14.0'
* 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 'BioSeqClass' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      2.9Mb
    scripts   3.0Mb
* 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
getTrain: warning in readFASTA(seqfile, strip.desc = TRUE): partial
  argument match of 'strip.desc' to 'strip.descs'
* checking Rd files ... NOTE
prepare_Rd: selectWeka.Rd:49-51: Dropping empty section \examples
* 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 ... 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 were 3 notes.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/BioSeqClass.Rcheck/00check.log'
for details.

* installing *source* package 'BioSeqClass' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'BioSeqClass.Rnw' 
** testing if installed package can be loaded

* DONE (BioSeqClass)

name	user	system	elapsed
basic	2.197	0.080	2.280
classify	11.090	0.434	12.759
featureAAindex	0.001	0.000	0.002
featureBDNAVIDEO	0.001	0.000	0.001
featureBinary	0.000	0.000	0.001
featureCKSAAP	0.001	0.000	0.001
featureCTD	0.001	0.001	0.001
featureDIPRODB	0.000	0.000	0.001
featureDOMAIN	0.001	0.001	0.001
featureEvaluate	0.025	0.001	0.026
featureFragmentComposition	0.001	0.000	0.001
featureGapPairComposition	0.001	0.000	0.001
featureHydro	0.001	0.000	0.001
featurePSSM	0.001	0.000	0.001
featurePseudoAAComp	0.000	0.001	0.001
featureSSC	0.003	0.000	0.004
hr	0.004	0.000	0.005
model	2.212	0.114	2.328
performance	2.344	0.049	2.397
selectFFS	1.002	0.022	1.025