BioC 3.5: CHECK report for PCAN on malbec2

Package: PCAN

Version: 1.4.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings PCAN_1.4.0.tar.gz

StartedAt: 2017-10-18 01:25:07 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:28:27 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 199.4 seconds

RetCode: 0

Status:  OK

CheckDir: PCAN.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings PCAN_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/PCAN.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.4.0’
* 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
compareHPSets  48.192  0.960  49.189
hpGeneHeatmap  48.216  0.140  48.380
hpGeneListComp 47.184  0.436  47.649
* 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	3.140	0.020	3.161
compareHPSets	48.192	0.960	49.189
computeHpIC	2.300	0.008	2.313
geneByHp	2.064	0.004	2.072
geneByTrait	0.036	0.004	0.040
geneDef	3.292	0.020	3.313
hpByTrait	3.500	0.016	3.519
hpDef	2.560	0.012	2.572
hpGeneHeatmap	48.216	0.140	48.380
hpGeneListComp	47.184	0.436	47.649
hpSetCompBestMatch	3.200	0.008	3.211
hpSetCompSummary	3.376	0.012	3.389
hp_ancestors	2.284	0.012	2.299
hp_class	0.052	0.000	0.052
hp_descendants	2.140	0.008	2.148
hqStrNw	0	0	0
hsEntrezByRPath	0	0	0
rPath	0.004	0.000	0.000
traitDef	3.060	0.012	3.076