BioC 2.14: CHECK report for dagLogo on petty

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

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

* 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)

name	user	system	elapsed
buildBackgroundModel	21.348	0.079	21.750
colorsets	0.002	0.000	0.001
dagHeatmap	7.630	0.034	7.786
dagLogo-package	15.181	0.803	16.739
dagLogo	14.723	0.787	18.351
ecoli.proteome	0.312	0.020	0.332
fetchSequence	0.270	0.011	13.248
formatSequence	0.002	0.000	0.003
nameHash	0.001	0.000	0.002
prepareProteome	0.001	0.000	0.002
proteome.example	0.094	0.010	0.105
seq.example	0.034	0.009	0.044
testDAU	20.865	0.055	21.005