BioC 2.14: CHECK report for KEGGprofile on petty

Package: KEGGprofile

Version: 1.7.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGprofile_1.7.6.tar.gz

StartedAt: 2014-10-07 22:40:44 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:45:27 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 282.7 seconds

RetCode: 0

Status:  OK

CheckDir: KEGGprofile.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGprofile_1.7.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/KEGGprofile.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.7.6’
* 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 ... [22s/22s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [47s/54s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
plot_pathway          18.920  1.073  21.639
plot_pathway_cor       6.253  0.248   6.983
find_enriched_pathway  5.752  0.158   5.939
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

* 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	0.070	0.005	0.076
convertId	0.289	0.019	2.648
download_KEGGfile	0.005	0.004	1.602
download_latest_pathway	0.001	0.000	0.002
find_enriched_pathway	5.752	0.158	5.939
newIdMatrix	0.004	0.000	0.004
parse_XMLfile	0.196	0.006	0.207
plot_pathway	18.920	1.073	21.639
plot_pathway_cor	6.253	0.248	6.983
plot_profile	3.583	0.192	4.739