Package: KEGGprofile

Version: 1.1.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings KEGGprofile_1.1.0.tar.gz

StartedAt: 2013-01-16 03:51:38 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 03:54:12 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 154.0 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGprofile.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/KEGGprofile.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGprofile/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGprofile’ version ‘1.1.0’
* 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 ‘KEGGprofile’ can be installed ... 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 ... NOTE
parse_XMLfile: warning in xmlTreeParse(paste(database_dir, "/", specis,
  pathway_id, ".xml", sep = ""), useInternal = TRUE): partial argument
  match of 'useInternal' to 'useInternalNodes'
plot_profile: no visible binding for global variable ‘x’
plot_profile: no visible binding for global variable ‘y’
* 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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plot_pathway          11.081  0.180  11.808
find_enriched_pathway  5.524  0.028   5.968
* 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
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/KEGGprofile.Rcheck/00check.log’
for details.

* installing *source* package ‘KEGGprofile’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘KEGGprofile.Rnw’ using ‘latin-9’ 
** testing if installed package can be loaded

* DONE (KEGGprofile)

name	user	system	elapsed
col_by_value	0.272	0.000	0.272
download_KEGGfile	0.004	0.004	1.477
find_enriched_pathway	5.524	0.028	5.968
parse_XMLfile	0.184	0.008	0.198
plot_pathway	11.081	0.180	11.808
plot_profile	1.820	0.040	1.863