BioC 3.3: CHECK report for PCAN on zin2

Package: PCAN

Version: 1.0.2

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings PCAN_1.0.2.tar.gz

StartedAt: 2016-10-13 05:07:15 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 05:10:49 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 214.4 seconds

RetCode: 0

Status:  OK

CheckDir: PCAN.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings PCAN_1.0.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/PCAN.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.0.2’
* 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  55.268  0.192  55.482
compareHPSets  53.442  0.220  56.187
hpGeneListComp 49.414  0.167  49.663
* 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	2.585	0.028	2.611
compareHPSets	53.442	0.220	56.187
computeHpIC	2.428	0.036	2.462
geneByHp	2.279	0.008	2.286
geneByTrait	0.044	0.004	0.047
geneDef	3.701	0.024	3.732
hpByTrait	3.609	0.008	3.616
hpDef	2.522	0.008	2.527
hpGeneHeatmap	55.268	0.192	55.482
hpGeneListComp	49.414	0.167	49.663
hpSetCompBestMatch	3.287	0.021	3.305
hpSetCompSummary	3.319	0.011	3.357
hp_ancestors	2.562	0.008	2.570
hp_class	0.051	0.000	0.052
hp_descendants	2.197	0.012	2.207
hqStrNw	0.001	0.000	0.000
hsEntrezByRPath	0	0	0
rPath	0	0	0
traitDef	3.326	0.016	3.340