BioC 2.13: CHECK report for seqLogo on zin1

Package: seqLogo

Version: 1.28.0

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings seqLogo_1.28.0.tar.gz

StartedAt: 2014-04-05 03:54:47 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:55:02 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 14.6 seconds

RetCode: 0

Status:  OK

CheckDir: seqLogo.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/seqLogo.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqLogo/DESCRIPTION’ ... OK
* this is package ‘seqLogo’ version ‘1.28.0’
* 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 ‘seqLogo’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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
‘library’ or ‘require’ call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
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 ‘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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘seqLogo.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [1s/1s] 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 4 notes.
See
  ‘/home/biocbuild/bbs-2.13-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
** testing if installed package can be loaded
* DONE (seqLogo)

name	user	system	elapsed
makePWM	0.016	0.000	0.013
seqLogo	0.076	0.000	0.078