Package: PCAN

Version: 1.12.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PCAN.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PCAN_1.12.0.tar.gz

StartedAt: 2019-10-16 03:49:49 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:53:33 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 224.7 seconds

RetCode: 0

Status:  OK

CheckDir: PCAN.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PCAN.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PCAN_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/PCAN.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.12.0’
* 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 56.078  0.428  56.531
compareHPSets  50.754  0.391  51.163
hpGeneHeatmap  47.211  0.308  47.519
* 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-3.9-bioc/R/bin/R CMD INSTALL PCAN
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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	2.61	0.06	2.67
compareHPSets	50.754	0.391	51.163
computeHpIC	1.674	0.016	1.690
geneByHp	1.701	0.020	1.721
geneByTrait	0.047	0.000	0.048
geneDef	2.413	0.020	2.433
hpByTrait	2.589	0.032	2.621
hpDef	1.998	0.032	2.031
hpGeneHeatmap	47.211	0.308	47.519
hpGeneListComp	56.078	0.428	56.531
hpSetCompBestMatch	3.224	0.044	3.268
hpSetCompSummary	2.942	0.036	2.978
hp_ancestors	2.640	0.016	2.656
hp_class	0.075	0.000	0.075
hp_descendants	2.534	0.036	2.571
hqStrNw	0	0	0
hsEntrezByRPath	0	0	0
rPath	0	0	0
traitDef	3.235	0.028	3.264