BioC 2.12: CHECK report for bgafun on george2

Package: bgafun

Version: 1.22.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings bgafun_1.22.0.tar.gz

StartedAt: 2013-10-09 00:22:22 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:23:49 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 86.7 seconds

RetCode: 0

Status:  OK

CheckDir: bgafun.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/bgafun.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... [3s/3s] 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 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 ... [49s/50s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
add_pseudo_counts      21.837  0.008  22.061
bgafun                  7.533  0.048   7.597
create_profile_strings  5.520  0.008   5.530
top_residues_2_groups   5.325  0.012   5.341
* 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
  ‘/home/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	0.488	0.008	0.505
add_pseudo_counts	21.837	0.008	22.061
average_cols_aap	1.460	0.000	1.463
bgafun	7.533	0.048	7.597
convert_aln_AAP	1.572	0.000	1.572
convert_aln_amino	1.388	0.008	1.395
create_profile_strings	5.520	0.008	5.530
remove_gaps_groups	1.468	0.008	1.477
run_between_pca	1.036	0.004	1.040
top_residues_2_groups	5.325	0.012	5.341