BioC 3.5: CHECK report for PCAN on toluca2

Package: PCAN

Version: 1.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PCAN_1.3.1.tar.gz

StartedAt: 2017-04-23 07:50:01 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 07:55:08 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 306.6 seconds

RetCode: 0

Status:  OK

CheckDir: PCAN.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 PCAN_1.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/PCAN.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PCAN/DESCRIPTION’ ... OK
* this is package ‘PCAN’ version ‘1.3.1’
* 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 ‘PCAN’ can be installed ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
hpGeneListComp 65.131  9.163  74.976
compareHPSets  68.169  5.941  80.247
hpGeneHeatmap  64.891  7.032  72.424
* 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
* DONE

Status: OK

* installing *source* package ‘PCAN’ ...
** 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 (PCAN)

name	user	system	elapsed
calcHpSim	3.298	0.064	3.384
compareHPSets	68.169	5.941	80.247
computeHpIC	2.824	0.129	2.961
geneByHp	2.552	0.186	2.750
geneByTrait	0.053	0.009	0.062
geneDef	4.195	0.313	4.536
hpByTrait	4.106	0.280	4.505
hpDef	2.651	0.181	2.851
hpGeneHeatmap	64.891	7.032	72.424
hpGeneListComp	65.131	9.163	74.976
hpSetCompBestMatch	3.951	0.526	4.502
hpSetCompSummary	4.129	0.389	4.566
hp_ancestors	2.937	0.183	3.146
hp_class	0.054	0.015	0.070
hp_descendants	2.268	0.173	2.442
hqStrNw	0.000	0.000	0.001
hsEntrezByRPath	0.000	0.000	0.001
rPath	0.000	0.000	0.001
traitDef	3.819	0.311	4.136