Package: bgafun

Version: 1.21.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch bgafun_1.21.0.tar.gz

StartedAt: 2013-03-25 01:20:38 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:22:06 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 88.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: bgafun.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/bgafun.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'bgafun/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'bgafun' version '1.21.0'
* 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] WARNING
Found the following significant warnings:
  Warning: '.path.package' is deprecated.
  Warning: '.path.package' is deprecated.
See '/Users/biocbuild/bbs-2.12-bioc/meat/bgafun.Rcheck/00install.out' for details.
* 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 ... [47s/48s] WARNING
Found the following significant warnings:

  Warning: '.path.package' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                        user system elapsed
add_pseudo_counts     21.422  0.032  21.456
bgafun                 6.116  0.316   6.455
top_residues_2_groups  5.398  0.167   5.581
* 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

WARNING: There were 2 warnings.
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
Warning: '.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** installing vignettes
   'bgafun.rnw' 
** testing if installed package can be loaded
Warning: '.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
* DONE (bgafun)

name	user	system	elapsed
Calculate_Row_Weights	0.249	0.028	0.278
add_pseudo_counts	21.422	0.032	21.456
average_cols_aap	1.598	0.021	1.619
bgafun	6.116	0.316	6.455
convert_aln_AAP	1.453	0.016	1.470
convert_aln_amino	1.563	0.209	1.792
create_profile_strings	4.601	0.148	4.761
remove_gaps_groups	1.383	0.198	1.617
run_between_pca	0.944	0.043	0.990
top_residues_2_groups	5.398	0.167	5.581