Package: bgafun

Version: 1.10.0

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings bgafun_1.10.0.tar.gz

StartedAt: 2010-10-04 16:10:49 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 16:12:08 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 79.6 seconds

RetCode: 0

Status:  OK

CheckDir: bgafun.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/bgafun.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bgafun/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bgafun' version '1.10.0'
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* 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	0.244	0.012	0.257
add_pseudo_counts	27.401	0.328	29.022
average_cols_aap	1.232	0.000	1.232
bgafun	7.449	0.040	7.506
convert_aln_AAP	1.220	0.000	1.217
convert_aln_amino	1.108	0.000	1.124
create_profile_strings	5.472	0.044	5.607
remove_gaps_groups	1.264	0.092	1.705
run_between_pca	1.256	0.084	1.567
top_residues_2_groups	5.641	0.460	8.164