Package: BioSeqClass

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BioSeqClass_1.18.0.tar.gz

StartedAt: 2013-05-01 02:55:01 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 03:00:02 -0700 (Wed, 01 May 2013)

EllapsedTime: 301.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BioSeqClass.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BioSeqClass.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BioSeqClass/DESCRIPTION' ... OK
* this is package 'BioSeqClass' version '1.18.0'
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'BioSeqClass' can be installed ... [21s/22s] 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 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 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 ... [45s/48s] WARNING
Found the following significant warnings:

  Warning: '.path.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
classify 18.431  0.641   20.14
* 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/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
** testing if installed package can be loaded
* DONE (BioSeqClass)

name	user	system	elapsed
basic	2.677	0.102	2.826
classify	18.431	0.641	20.140
featureAAindex	0.019	0.008	0.028
featureBDNAVIDEO	0.297	0.014	0.318
featureBinary	0.004	0.007	0.014
featureCKSAAP	0.004	0.006	0.011
featureCTD	0.009	0.008	0.017
featureDIPRODB	0.009	0.008	0.017
featureDOMAIN	0.002	0.005	0.008
featureEvaluate	0.047	0.026	0.074
featureFragmentComposition	0.003	0.005	0.009
featureGapPairComposition	0.010	0.007	0.016
featureHydro	0.010	0.008	0.018
featurePSSM	0.003	0.006	0.009
featurePseudoAAComp	0.003	0.006	0.008
featureSSC	0.007	0.008	0.015
hr	0.015	0.015	0.030
model	3.488	0.103	4.047
performance	4.446	0.087	4.680
selectFFS	1.116	0.078	1.228