Package: bgafun

Version: 1.15.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings bgafun_1.15.0.tar.gz

StartedAt: 2011-05-09 12:40:07 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 12:41:27 -0700 (Mon, 09 May 2011)

EllapsedTime: 80.0 seconds

RetCode: 0

Status:  OK

CheckDir: bgafun.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/bgafun.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bgafun/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bgafun' version '1.15.0'
* 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 installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... 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 vignettes ... 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:stats':

    nobs

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 ...
*** tangling vignette sources ...
   'bgafun.rnw' 
** testing if installed package can be loaded

* DONE (bgafun)

name	user	system	elapsed
Calculate_Row_Weights	0.26	0.02	0.28
add_pseudo_counts	22.53	0.00	22.63
average_cols_aap	1.27	0.01	1.28
bgafun	6.91	0.02	6.92
convert_aln_AAP	1.29	0.00	1.30
convert_aln_amino	1.27	0.00	1.26
create_profile_strings	4.73	0.00	4.78
remove_gaps_groups	1.34	0.00	1.34
run_between_pca	1.13	0.01	1.16
top_residues_2_groups	4.98	0.02	5.02