BioC 2.14: CHECK report for dagLogo on moscato2

Package: dagLogo

Version: 1.2.1

Command: E:\biocbld\bbs-2.14-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings dagLogo_1.2.1.tar.gz

StartedAt: 2014-10-08 00:21:00 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 00:26:13 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 313.2 seconds

RetCode: 0

Status:  OK

CheckDir: dagLogo.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbld\bbs-2.14-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings dagLogo_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/dagLogo.Rcheck'
* using R version 3.1.1 (2014-07-10)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'dagLogo' can be installed ... [18s] 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 ... [56s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
testDAU              9.60   0.02    9.62
buildBackgroundModel 8.86   0.00    8.87
dagLogo-package      4.69   0.06   10.66
dagLogo              4.59   0.07    9.90
fetchSequence        0.61   0.11    5.48
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'runTests.R' [18s]
 [18s] 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
  'E:/biocbld/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	8.86	0.00	8.87
colorsets	0	0	0
dagHeatmap	3.39	0.00	3.38
dagLogo-package	4.69	0.06	10.66
dagLogo	4.59	0.07	9.90
ecoli.proteome	0.20	0.01	0.22
fetchSequence	0.61	0.11	5.48
formatSequence	0	0	0
nameHash	0	0	0
prepareProteome	0	0	0
proteome.example	0.09	0.00	0.09
seq.example	0.03	0.00	0.04
testDAU	9.60	0.02	9.62