BioC 3.5: CHECK report for Pi on veracruz2

Package: Pi

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Pi_1.4.0.tar.gz

StartedAt: 2017-10-18 07:17:23 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 07:24:00 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 396.6 seconds

RetCode: 0

Status:  OK

CheckDir: Pi.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Pi_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Pi.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Pi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Pi’ 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 ‘Pi’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Pi.Rcheck/00check.log’
for details.

* installing *source* package ‘Pi’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Pi)

name	user	system	elapsed
cTarget	0.001	0.000	0.001
dTarget	0.001	0.000	0.001
eGSEA	0.001	0.000	0.001
eTarget	0	0	0
pNode	0.001	0.000	0.001
pPerf	0.001	0.000	0.001
sGS	0.001	0.000	0.000
sTarget	0.001	0.001	0.001
xContour	0.030	0.001	0.031
xGSEAbarplot	0.001	0.000	0.000
xGSEAconciser	0.001	0.000	0.001
xGSEAdotplot	0.001	0.000	0.002
xGSsimulator	0.001	0.000	0.001
xMLcaret	0.001	0.000	0.001
xMLcompare	0.001	0.000	0.001
xMLdensity	0.001	0.000	0.002
xMLdotplot	0.001	0.001	0.001
xMLfeatureplot	0.001	0.000	0.001
xMLglmnet	0.001	0.000	0.001
xMLparameters	0.001	0.000	0.001
xMLrandomforest	0.001	0.000	0.001
xMLzoom	0.001	0.000	0.001
xPCHiCplot	0.105	0.011	0.683
xPier	0.002	0.000	0.002
xPierAnno	0.209	0.010	1.391
xPierCross	0.000	0.000	0.001
xPierEvidence	0.001	0.001	0.000
xPierGSEA	0.001	0.000	0.002
xPierGenes	0.098	0.012	1.216
xPierManhattan	0.002	0.000	0.002
xPierMatrix	0.001	0.000	0.001
xPierPathways	0.001	0.000	0.002
xPierROCR	0.000	0.000	0.001
xPierSNPs	0.138	0.010	1.259
xPierSNPsAdv	0.201	0.012	1.318
xPierSNPsConsensus	0.102	0.012	1.219
xPierSubnet	0.103	0.013	1.282
xPierTrack	0.108	0.013	1.285
xPierTrackAdv	0.111	0.012	1.228
xPredictCompare	0.000	0.001	0.001
xPredictROCR	0.001	0.000	0.000
xRWR	0.002	0.000	0.002
xSNP2cGenes	0.086	0.011	1.206
xSNP2eGenes	0.092	0.010	1.212
xSNPeqtl	0.099	0.012	1.219
xSNPhic	0.102	0.012	1.221
xVisEvidence	0.001	0.001	0.001