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BioC 3.0: CHECK report for seqLogo on perceval

This page was generated on 2015-04-10 09:53:20 -0700 (Fri, 10 Apr 2015).

Package 812/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqLogo 1.32.1
Oliver Bembom
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/seqLogo
Last Changed Rev: 96121 / Revision: 102249
Last Changed Date: 2014-10-28 11:33:55 -0700 (Tue, 28 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ WARNINGS ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: seqLogo
Version: 1.32.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch seqLogo_1.32.1.tar.gz
StartedAt: 2015-04-10 06:17:21 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 06:17:51 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 29.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: seqLogo.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch seqLogo_1.32.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/seqLogo.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqLogo/DESCRIPTION’ ... OK
* this is package ‘seqLogo’ version ‘1.32.1’
* 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 ... [2s/2s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘graphics::plot’ when loading ‘seqLogo’
See ‘/Users/biocbuild/bbs-3.0-bioc/meat/seqLogo.Rcheck/00install.out’ for details.
* 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.
* 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 ... WARNING
Undocumented S4 methods:
  generic 'plot' and siglist 'pwm,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* 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
* DONE

WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/seqLogo.Rcheck/00check.log’
for details.

seqLogo.Rcheck/00install.out:

* installing *source* package ‘seqLogo’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::plot’ when loading ‘seqLogo’
Creating a generic function for ‘plot’ from package ‘graphics’ 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
Warning: replacing previous import by ‘graphics::plot’ when loading ‘seqLogo’
* DONE (seqLogo)

seqLogo.Rcheck/seqLogo-Ex.timings:

nameusersystemelapsed
makePWM0.0160.0040.020
seqLogo0.1610.0060.167