Package: KEGGprofile

Version: 1.0.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings KEGGprofile_1.0.0.tar.gz

StartedAt: 2013-03-25 02:35:04 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:37:17 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 133.1 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGprofile.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/KEGGprofile.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.0.0’
* 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 whether package ‘KEGGprofile’ can be installed ... OK
* checking installed package size ... 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 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          9.285  0.104   9.418
find_enriched_pathway 5.236  0.048   5.303
* 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-2.11-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	0.032	0.000	0.035
download_KEGGfile	0.000	0.004	1.358
find_enriched_pathway	5.236	0.048	5.303
parse_XMLfile	0.116	0.004	0.136
plot_pathway	9.285	0.104	9.418
plot_profile	2.080	0.012	2.095