Package: PCAN

Version: 1.10.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:PCAN.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings PCAN_1.10.0.tar.gz

StartedAt: 2019-04-16 02:01:32 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:05:34 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 241.6 seconds

RetCode: 0

Status:  OK

CheckDir: PCAN.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:PCAN.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings PCAN_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/PCAN.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.10.0’
* 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 or elapsed time > 5s
                 user system elapsed
hpGeneListComp 61.604  0.320  61.988
compareHPSets  58.792  0.560  59.487
hpGeneHeatmap  58.260  0.604  58.957
* 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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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL PCAN
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘PCAN’ ...
** 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
* DONE (PCAN)

name	user	system	elapsed
calcHpSim	2.828	0.052	2.936
compareHPSets	58.792	0.560	59.487
computeHpIC	2.272	0.016	2.290
geneByHp	2.900	0.020	2.926
geneByTrait	0.064	0.004	0.071
geneDef	3.852	0.028	3.883
hpByTrait	4.048	0.024	4.077
hpDef	2.396	0.020	2.418
hpGeneHeatmap	58.260	0.604	58.957
hpGeneListComp	61.604	0.320	61.988
hpSetCompBestMatch	4.632	0.032	4.668
hpSetCompSummary	4.496	0.040	4.570
hp_ancestors	2.672	0.032	2.706
hp_class	0.048	0.004	0.061
hp_descendants	2.508	0.040	2.547
hqStrNw	0	0	0
hsEntrezByRPath	0	0	0
rPath	0	0	0
traitDef	4.212	0.056	4.276