Package: KEGGprofile

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGprofile_1.2.0.tar.gz

StartedAt: 2013-05-01 07:20:32 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 07:23:36 -0700 (Wed, 01 May 2013)

EllapsedTime: 183.5 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGprofile.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/KEGGprofile.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'KEGGprofile/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGprofile' version '1.2.0'
* 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 ... [15s/15s] 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 ... [33s/36s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plot_pathway          14.681  1.131  16.320
find_enriched_pathway  6.127  0.257   6.531
* 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
  '/Users/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
** testing if installed package can be loaded
* DONE (KEGGprofile)

name	user	system	elapsed
col_by_value	0.059	0.005	0.064
download_KEGGfile	0.008	0.007	1.350
find_enriched_pathway	6.127	0.257	6.531
parse_XMLfile	0.166	0.006	0.189
plot_pathway	14.681	1.131	16.320
plot_profile	3.111	0.267	3.565