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BioC 2.14: CHECK report for dagLogo on petty

This page was generated on 2014-10-08 09:01:21 -0700 (Wed, 08 Oct 2014).

Package 206/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dagLogo 1.2.1
Jianhong Ou
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/dagLogo
Last Changed Rev: 93264 / Revision: 95116
Last Changed Date: 2014-08-08 14:15:21 -0700 (Fri, 08 Aug 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: dagLogo
Version: 1.2.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch dagLogo_1.2.1.tar.gz
StartedAt: 2014-10-07 21:34:58 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:44:20 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 562.0 seconds
RetCode: 0
Status:  OK 
CheckDir: dagLogo.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch dagLogo_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/dagLogo.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dagLogo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dagLogo’ 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘dagLogo’ can be installed ... [33s/35s] 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [98s/115s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
buildBackgroundModel 21.348  0.079  21.750
testDAU              20.865  0.055  21.005
dagLogo-package      15.181  0.803  16.739
dagLogo              14.723  0.787  18.351
dagHeatmap            7.630  0.034   7.786
fetchSequence         0.270  0.011  13.248
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [38s/38s]
 [38s/39s] 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 was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/dagLogo.Rcheck/00check.log’
for details.

dagLogo.Rcheck/00install.out:

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

dagLogo.Rcheck/dagLogo-Ex.timings:

nameusersystemelapsed
buildBackgroundModel21.348 0.07921.750
colorsets0.0020.0000.001
dagHeatmap7.6300.0347.786
dagLogo-package15.181 0.80316.739
dagLogo14.723 0.78718.351
ecoli.proteome0.3120.0200.332
fetchSequence 0.270 0.01113.248
formatSequence0.0020.0000.003
nameHash0.0010.0000.002
prepareProteome0.0010.0000.002
proteome.example0.0940.0100.105
seq.example0.0340.0090.044
testDAU20.865 0.05521.005