Package: PCAN

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PCAN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PCAN_1.15.0.tar.gz

StartedAt: 2020-01-16 07:19:29 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:26:57 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 448.1 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 --install=check:PCAN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PCAN_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/PCAN.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PCAN/DESCRIPTION’ ... OK
* this is package ‘PCAN’ version ‘1.15.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
compareHPSets      93.975 21.398 116.423
hpGeneHeatmap      92.619 21.988 114.663
hpGeneListComp     91.348 21.254 112.614
hpByTrait           4.707  0.629   5.337
hpSetCompSummary    4.609  0.615   5.228
geneDef             4.495  0.652   5.147
hpSetCompBestMatch  4.337  0.735   5.072
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PCAN
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘PCAN’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PCAN)

name	user	system	elapsed
calcHpSim	3.111	0.500	3.611
compareHPSets	93.975	21.398	116.423
computeHpIC	2.925	0.424	3.350
geneByHp	3.030	0.415	3.446
geneByTrait	0.064	0.009	0.072
geneDef	4.495	0.652	5.147
hpByTrait	4.707	0.629	5.337
hpDef	3.259	0.453	3.712
hpGeneHeatmap	92.619	21.988	114.663
hpGeneListComp	91.348	21.254	112.614
hpSetCompBestMatch	4.337	0.735	5.072
hpSetCompSummary	4.609	0.615	5.228
hp_ancestors	2.816	0.406	3.222
hp_class	0.061	0.011	0.072
hp_descendants	2.794	0.356	3.150
hqStrNw	0.000	0.000	0.001
hsEntrezByRPath	0	0	0
rPath	0	0	0
traitDef	4.230	0.617	4.847