BioC 3.4: CHECK report for PCAN on morelia

Package: PCAN

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PCAN_1.2.1.tar.gz

StartedAt: 2017-04-15 06:04:44 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 06:09:51 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 307.6 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_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/PCAN.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.1’
* 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
hpGeneHeatmap  75.575  5.861  81.510
compareHPSets  73.206  5.996  79.270
hpGeneListComp 69.776  9.099  78.944
* 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	3.047	0.062	3.111
compareHPSets	73.206	5.996	79.270
computeHpIC	2.578	0.140	2.719
geneByHp	2.572	0.101	2.676
geneByTrait	0.056	0.014	0.071
geneDef	3.799	0.234	4.035
hpByTrait	3.981	0.205	4.188
hpDef	3.034	0.118	3.155
hpGeneHeatmap	75.575	5.861	81.510
hpGeneListComp	69.776	9.099	78.944
hpSetCompBestMatch	3.821	0.380	4.206
hpSetCompSummary	3.855	0.290	4.148
hp_ancestors	3.077	0.121	3.204
hp_class	0.062	0.020	0.081
hp_descendants	2.612	0.136	2.751
hqStrNw	0.001	0.000	0.001
hsEntrezByRPath	0.000	0.000	0.001
rPath	0.000	0.000	0.001
traitDef	4.034	0.198	4.236