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BioC 2.12: CHECK report for motifRG on george2

This page was generated on 2013-10-09 09:37:53 -0700 (Wed, 09 Oct 2013).

Package 426/671HostnameOS / ArchBUILDCHECKBUILD BIN
motifRG 1.4.0
Zizhen Yao
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/motifRG
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: motifRG
Version: 1.4.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings motifRG_1.4.0.tar.gz
StartedAt: 2013-10-09 03:27:36 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 03:34:09 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 392.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: motifRG.Rcheck
Warnings: 1

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/motifRG.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifRG/DESCRIPTION’ ... OK
* this is package ‘motifRG’ version ‘1.4.0’
* 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 ‘motifRG’ can be installed ... [16s/19s] OK
* checking installed package size ... OK
* checking package 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 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
matchPWMCoor: no visible global function definition for ‘GRanges’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'findMotif':
findMotif
  Code: function(all.seq, category, weights = rep(1, length(all.seq)),
                 start.width = 6, min.cutoff = 5, min.ratio = 1.3,
                 min.frac = 0.01, both.strand = T, flank = 2, max.motif
                 = 5, mask = T, other.data = NULL, start.nmer = NULL,
                 enriched.only = F, n.bootstrap = 5, bootstrap.pvalue =
                 0.1, is.parallel = T, mc.cores = 4, min.info = 10,
                 max.width = 15, discretize = T)
  Docs: function(all.seq, category, weights = rep(1, length(all.seq)),
                 start.width = 6, min.cutoff = 5, min.ratio = 1.3,
                 min.frac = 0.01, both.strand = T, flank = 2, max.motif
                 = 5, mask = T, other.data = NULL, start.nmer = NULL,
                 enriched.only = F, n.bootstrap = 5, bootstrap.pvalue =
                 0.1, is.parallel = T, mc.cores = 4, min.info = 10,
                 max.width = 15, discretize = TRUE)
  Mismatches in argument default values:
    Name: 'discretize' Code: T Docs: TRUE

* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [153s/108s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
findMotif      108.086 26.857  85.170
refinePWMMotif   8.841  0.100   9.944
* 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/motifRG.Rcheck/00check.log’
for details.

motifRG.Rcheck/00install.out:

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

motifRG.Rcheck/motifRG-Ex.timings:

nameusersystemelapsed
control.seq0.1520.0080.163
ctcf.seq0.1280.0040.134
findMotif108.086 26.857 85.170
motifLatexTable0.4720.0800.689
plotMotif0.1520.0120.169
refinePWMMotif8.8410.1009.944
summaryMotif0.1120.0000.114