BioC 2.12: CHECK report for bgafun on petty

Package: bgafun

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch bgafun_1.22.0.tar.gz

StartedAt: 2013-10-08 21:40:05 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:41:56 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 110.8 seconds

RetCode: 0

Status:  OK

CheckDir: bgafun.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/bgafun.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'bgafun/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bgafun' version '1.22.0'
* 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 'bgafun' can be installed ... [4s/4s] 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 ... 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' ... NOTE
The following files should probably not be installed:
  'mystyle.bst'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [62s/63s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
add_pseudo_counts      28.861  0.112  29.128
bgafun                  8.635  0.157   8.819
top_residues_2_groups   6.252  0.075   6.936
create_profile_strings  6.048  0.112   6.189
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/bgafun.Rcheck/00check.log'
for details.

* installing *source* package 'bgafun' ...
** 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 (bgafun)

name	user	system	elapsed
Calculate_Row_Weights	0.537	0.018	0.557
add_pseudo_counts	28.861	0.112	29.128
average_cols_aap	1.940	0.027	1.969
bgafun	8.635	0.157	8.819
convert_aln_AAP	1.957	0.012	1.986
convert_aln_amino	1.858	0.042	1.902
create_profile_strings	6.048	0.112	6.189
remove_gaps_groups	1.968	0.045	2.019
run_between_pca	1.489	0.025	1.521
top_residues_2_groups	6.252	0.075	6.936