BioC 3.6: CHECK report for PCAN on malbec1

Package: PCAN

Version: 1.5.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PCAN_1.5.0.tar.gz

StartedAt: 2017-08-16 01:19:23 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:22:31 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 188.0 seconds

RetCode: 0

Status:  OK

CheckDir: PCAN.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings PCAN_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/PCAN.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PCAN/DESCRIPTION’ ... OK
* this is package ‘PCAN’ version ‘1.5.0’
* 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 ‘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  46.520  0.176  46.723
compareHPSets  45.856  0.440  46.320
hpGeneListComp 44.160  0.304  44.489
* 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	2.704	0.016	2.727
compareHPSets	45.856	0.440	46.320
computeHpIC	1.996	0.012	2.007
geneByHp	2.012	0.000	2.014
geneByTrait	0.040	0.000	0.039
geneDef	2.960	0.016	2.978
hpByTrait	3.160	0.008	3.172
hpDef	2.308	0.004	2.315
hpGeneHeatmap	46.520	0.176	46.723
hpGeneListComp	44.160	0.304	44.489
hpSetCompBestMatch	2.968	0.020	2.989
hpSetCompSummary	3.084	0.012	3.097
hp_ancestors	2.152	0.008	2.160
hp_class	0.044	0.004	0.049
hp_descendants	2.208	0.004	2.213
hqStrNw	0	0	0
hsEntrezByRPath	0.000	0.000	0.001
rPath	0.000	0.000	0.001
traitDef	3.004	0.020	3.026