BioC 2.14: CHECK report for dagLogo on zin2

Package: dagLogo

Version: 1.2.1

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings dagLogo_1.2.1.tar.gz

StartedAt: 2014-10-07 23:00:07 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:04:46 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 278.9 seconds

RetCode: 0

Status:  OK

CheckDir: dagLogo.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings dagLogo_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/dagLogo.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (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 ... [15s/16s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [42s/74s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
testDAU              9.021  0.044   9.076
buildBackgroundModel 8.824  0.012   8.849
dagLogo              6.316  0.568   7.071
dagLogo-package      6.120  0.564   6.906
fetchSequence        0.120  0.008  31.275
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [17s/17s]
 [17s/17s] 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
  ‘/home/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	8.824	0.012	8.849
colorsets	0.000	0.000	0.001
dagHeatmap	3.117	0.004	3.123
dagLogo-package	6.120	0.564	6.906
dagLogo	6.316	0.568	7.071
ecoli.proteome	0.168	0.000	0.167
fetchSequence	0.120	0.008	31.275
formatSequence	0.000	0.000	0.001
nameHash	0.000	0.000	0.001
prepareProteome	0	0	0
proteome.example	0.048	0.000	0.051
seq.example	0.020	0.000	0.017
testDAU	9.021	0.044	9.076