BioC 2.13: CHECK report for RTopper on perceval

Package: RTopper

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RTopper_1.8.0.tar.gz

StartedAt: 2014-04-05 04:12:29 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:14:28 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 118.6 seconds

RetCode: 0

Status:  OK

CheckDir: RTopper.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/RTopper.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RTopper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTopper’ version ‘1.8.0’
* 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 ‘RTopper’ can be installed ... [6s/6s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘limma’
A package should be listed in only one of these fields.
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘preamble.tex’, ‘subfigure.sty’, ‘vmargin.sty’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘RTopper.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [48s/49s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
computeDrStat 33.817  1.288  36.392
convertToDr    9.021  0.053   9.193
* 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 4 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/RTopper.Rcheck/00check.log’
for details.

* installing *source* package ‘RTopper’ ...
** 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 (RTopper)

name	user	system	elapsed
adjustPvalGSE	0.041	0.003	0.043
combineGSE	0.021	0.001	0.022
computeDrStat	33.817	1.288	36.392
convertToDr	9.021	0.053	9.193
dat	0.121	0.011	0.133
fgsList	0.030	0.003	0.033
gseResultsSep	0.030	0.002	0.031
intScores	0.017	0.001	0.018
pheno	0.114	0.010	0.125
runBatchGSE	0.273	0.014	0.290
sepScores	0.017	0.003	0.021