BioC 3.5: CHECK report for Pi on toluca2

Package: Pi

Version: 1.3.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Pi_1.3.3.tar.gz

StartedAt: 2017-04-23 07:58:18 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 08:04:54 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 396.8 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_1.3.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Pi.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.3.3’
* 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  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
* 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	0.001	0.001
dTarget	0	0	0
eGSEA	0.001	0.000	0.000
eTarget	0.001	0.000	0.001
pNode	0	0	0
pPerf	0.001	0.000	0.000
sGS	0.001	0.000	0.001
sTarget	0.001	0.000	0.001
xContour	0.032	0.002	0.033
xGSEAbarplot	0.001	0.000	0.001
xGSEAconciser	0.000	0.000	0.001
xGSEAdotplot	0.001	0.000	0.001
xGSsimulator	0.000	0.000	0.001
xMLcaret	0.001	0.000	0.000
xMLcompare	0	0	0
xMLdensity	0.001	0.000	0.000
xMLdotplot	0.001	0.000	0.001
xMLfeatureplot	0.000	0.001	0.001
xMLglmnet	0.000	0.000	0.001
xMLparameters	0.000	0.000	0.001
xMLrandomforest	0.000	0.000	0.001
xMLzoom	0.000	0.001	0.001
xPCHiCplot	0.101	0.024	0.676
xPier	0.002	0.000	0.001
xPierAnno	0.223	0.030	0.805
xPierCross	0.000	0.000	0.001
xPierEvidence	0.001	0.000	0.000
xPierGSEA	0.001	0.000	0.001
xPierGenes	0.102	0.023	0.674
xPierManhattan	0.001	0.000	0.003
xPierMatrix	0.001	0.000	0.001
xPierPathways	0.002	0.000	0.002
xPierROCR	0.001	0.001	0.001
xPierSNPs	0.130	0.026	0.706
xPierSNPsAdv	0.224	0.039	0.813
xPierSNPsConsensus	0.115	0.027	0.691
xPierSubnet	0.118	0.025	0.697
xPierTrack	0.115	0.027	0.693
xPierTrackAdv	0.113	0.029	0.696
xPredictCompare	0.001	0.000	0.001
xPredictROCR	0.000	0.000	0.001
xRWR	0.002	0.000	0.003
xSNP2cGenes	0.106	0.026	0.682
xSNP2eGenes	0.117	0.028	0.694
xSNPeqtl	0.121	0.028	0.697
xSNPhic	0.116	0.026	0.691
xVisEvidence	0.001	0.000	0.001