Package: seqLogo

Version: 1.22.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings seqLogo_1.22.0.tar.gz

StartedAt: 2012-04-01 03:23:07 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 03:23:23 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 15.7 seconds

RetCode: 0

Status:  OK

CheckDir: seqLogo.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/seqLogo.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'seqLogo/DESCRIPTION' ... OK
* this is package 'seqLogo' version '1.22.0'
* 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 'seqLogo' can be installed ... OK
* checking installed package size ... OK
* 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
File 'seqLogo/R/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

* checking Rd files ... NOTE
prepare_Rd: makePWM.Rd:17-18: Dropping empty section \details
prepare_Rd: makePWM.Rd:25-26: Dropping empty section \seealso
prepare_Rd: pwm-class.Rd:49: Dropping empty section \note
prepare_Rd: pwm-class.Rd:46: Dropping empty section \references
prepare_Rd: pwm-class.Rd:52-53: Dropping empty section \seealso
prepare_Rd: pwm-class.Rd:54-55: Dropping empty section \examples
prepare_Rd: seqLogo.Rd:34: Dropping empty section \note
prepare_Rd: seqLogo.Rd:32: Dropping empty section \references
prepare_Rd: seqLogo.Rd:36: Dropping empty section \seealso
* 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
* 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 2 notes.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/seqLogo.Rcheck/00check.log'
for details.

* installing *source* package 'seqLogo' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'seqLogo'
Creating a generic function for 'summary' from package 'base' in package 'seqLogo'
Creating a generic function for 'print' from package 'base' in package 'seqLogo'
** help
*** installing help indices
** building package indices
** installing vignettes
   'seqLogo.Rnw' 
** testing if installed package can be loaded

* DONE (seqLogo)

name	user	system	elapsed
makePWM	0.008	0.000	0.013
seqLogo	0.108	0.012	0.121