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BioC 3.3: CHECK report for DiffLogo on zin2

This page was generated on 2016-10-13 12:46:00 -0700 (Thu, 13 Oct 2016).

Package 303/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffLogo 1.2.1
Hendrik Treutler
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/DiffLogo
Last Changed Rev: 117513 / Revision: 122332
Last Changed Date: 2016-05-15 13:18:19 -0700 (Sun, 15 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DiffLogo
Version: 1.2.1
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DiffLogo_1.2.1.tar.gz
StartedAt: 2016-10-13 01:20:48 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:21:10 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 22.0 seconds
RetCode: 0
Status:  OK 
CheckDir: DiffLogo.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings DiffLogo_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/DiffLogo.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DiffLogo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DiffLogo’ version ‘1.2.1’
* 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 ‘DiffLogo’ can be installed ... 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 loading without being on the library search path ... 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 ... NOTE
diffLogo: no visible global function definition for ‘plot’
diffLogo: no visible global function definition for ‘axis’
diffLogo: no visible global function definition for ‘polygon’
diffLogo: no visible global function definition for ‘lines’
diffLogoTable: no visible global function definition for ‘plot.new’
diffLogoTable: no visible global function definition for
  ‘colorRampPalette’
diffLogoTable: no visible global function definition for ‘rgb’
diffLogoTable: no visible global function definition for ‘dist’
diffLogoTable: no visible global function definition for ‘hclust’
diffLogoTable: no visible global function definition for ‘par’
diffLogoTable: no visible global function definition for ‘plot’
diffLogoTable: no visible global function definition for ‘rect’
diffLogoTable: no visible global function definition for ‘axis’
seqLogo: no visible global function definition for ‘plot’
seqLogo: no visible global function definition for ‘abline’
seqLogo: no visible global function definition for ‘axis’
seqLogo: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  abline axis colorRampPalette dist hclust lines par plot plot.new
  polygon rect rgb
Consider adding
  importFrom("grDevices", "colorRampPalette", "rgb")
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "plot.new", "polygon", "rect")
  importFrom("stats", "dist", "hclust")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/DiffLogo.Rcheck/00check.log’
for details.


DiffLogo.Rcheck/00install.out:

* installing *source* package ‘DiffLogo’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DiffLogo)

DiffLogo.Rcheck/DiffLogo-Ex.timings:

nameusersystemelapsed
ASN0.2220.0040.226
Alphabet000
DNA0.0890.0000.089
createDiffLogoObject0.0580.0040.062
diffLogo0.0620.0000.062
diffLogoFromPwm0.0520.0040.056
diffLogoTable0.7180.0070.728
differenceOfICs0.3290.0090.336
getPwmFromAlignment0.2160.0040.219
informationContent0.0870.0000.087
lossOfAbsICDifferences0.0580.0040.062
normalizedDifferenceOfProbabilities0.0620.0030.065
probabilities0.080.000.08
seqLogo0.0510.0000.052
shannonDivergence0.0590.0000.060
sumOfAbsICDifferences0.0630.0000.062
sumOfAbsProbabilityDifferences0.0620.0000.062
sumProbabilities0.0540.0000.054