BioC 3.3: CHECK report for PCAN on morelia

Package: PCAN

Version: 0.99.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PCAN_0.99.4.tar.gz

StartedAt: 2016-04-21 05:56:57 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 06:01:43 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 285.9 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_0.99.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/PCAN.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘0.99.4’
* 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 ... [1s/1s] 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 ... [259s/259s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
compareHPSets  77.375  5.828  83.315
hpGeneHeatmap  64.965  5.856  70.867
hpGeneListComp 59.511  9.109  68.653
* 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	2.911	0.046	2.961
compareHPSets	77.375	5.828	83.315
computeHpIC	2.511	0.142	2.656
geneByHp	2.455	0.120	2.579
geneByTrait	0.051	0.010	0.061
geneDef	4.234	0.253	4.499
hpByTrait	3.767	0.228	3.997
hpDef	2.841	0.169	3.014
hpGeneHeatmap	64.965	5.856	70.867
hpGeneListComp	59.511	9.109	68.653
hpSetCompBestMatch	3.372	0.357	3.732
hpSetCompSummary	3.114	0.296	3.412
hp_ancestors	2.281	0.154	2.436
hp_class	0.053	0.010	0.063
hp_descendants	2.064	0.195	2.260
hqStrNw	0	0	0
hsEntrezByRPath	0.000	0.000	0.001
rPath	0.001	0.000	0.000
traitDef	3.972	0.229	4.207