BioC 2.13: CHECK report for dualKS on zin1

Package: dualKS

Version: 1.21.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings dualKS_1.21.0.tar.gz

StartedAt: 2013-10-08 00:15:10 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 00:15:52 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 42.2 seconds

RetCode: 0

Status:  OK

CheckDir: dualKS.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/dualKS.Rcheck’
* using R version 3.0.2 (2013-09-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dualKS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dualKS’ version ‘1.21.0’
* 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 ‘dualKS’ can be installed ... [3s/3s] 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’
  These packages needs to imported from for the case when
  this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘dualKS/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(paste(msg, collapse = "\n"))

See section ‘Good practice’ in '?.onAttach'.

dksToGeneSet : .rank: warning in rank(-x, ties = "first"): partial
  argument match of 'ties' to 'ties.method'
* 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 ... [11s/11s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/dualKS.Rcheck/00check.log’
for details.

* installing *source* package ‘dualKS’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘dualKS’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘dualKS’
** help
*** installing help indices
** building package indices
*** Deprecation warning ***: Package 'dualKS' is deprecated and will
    not be supported after Bioconductor release 2.11.
** installing vignettes
** testing if installed package can be loaded
* DONE (dualKS)

name	user	system	elapsed
KS	2.388	0.004	2.394
dksClassify	1.252	0.004	1.258
dksCustomClass	0.020	0.000	0.021
dksPerm	1.260	0.000	1.261
dksSelectGenes	1.244	0.000	1.245
dksTrain	1.316	0.000	1.319
dksWeights	1.900	0.000	1.903