Package: bgafun

Version: 1.12.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings bgafun_1.12.0.tar.gz

StartedAt: 2011-03-31 04:32:59 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 04:34:04 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 64.6 seconds

RetCode: 0

Status:  OK

CheckDir: bgafun.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/bgafun.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘1.12.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘bgafun’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘bgafun’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: ade4

Attaching package: 'ade4'

The following object(s) are masked from 'package:base':

    within

Loading required package: RColorBrewer
Loading required package: gplots
Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: 'gdata'

The following object(s) are masked from 'package:utils':

    object.size

Loading required package: caTools
Loading required package: bitops
Loading required package: grid

Attaching package: 'gplots'

The following object(s) are masked from 'package:stats':

    lowess

Loading required package: scatterplot3d
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (bgafun)

name	user	system	elapsed
Calculate_Row_Weights	0.236	0.004	0.241
add_pseudo_counts	22.821	0.004	22.824
average_cols_aap	1.068	0.000	1.068
bgafun	6.712	0.036	6.752
convert_aln_AAP	1.085	0.000	1.082
convert_aln_amino	1.012	0.004	1.017
create_profile_strings	4.668	0.000	4.668
remove_gaps_groups	1.112	0.004	1.116
run_between_pca	1.056	0.000	1.065
top_residues_2_groups	4.796	0.012	4.811