BioC 3.4: CHECK report for Pi on morelia

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Pi_1.2.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/Pi.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.2.1’
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘Pi’
  Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘Pi’
See ‘/Users/biocbuild/bbs-3.4-bioc/meat/Pi.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.6Mb
  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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/Pi.Rcheck/00check.log’
for details.

* installing *source* package ‘Pi’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘Pi’
Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘Pi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘Pi’
Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘Pi’
* DONE (Pi)

name	user	system	elapsed
xContour	0.017	0.002	0.019
xGSsimulator	0.001	0.000	0.001
xMLdensity	0.001	0.000	0.001
xMLdotplot	0.000	0.000	0.001
xMLrandomforest	0	0	0
xPCHiCplot	0.391	0.012	1.550
xPier	0.001	0.000	0.002
xPierGenes	0.125	0.012	1.286
xPierManhattan	0.157	0.010	1.317
xPierMatrix	0.001	0.000	0.001
xPierPathways	0.123	0.012	1.282
xPierSNPs	0.121	0.010	1.282
xPierSNPsAdv	0.126	0.010	1.285
xPierSNPsConsensus	0.084	0.009	1.253
xPierSubnet	0.127	0.013	1.289
xPierTrack	0.099	0.009	1.255
xPredictCompare	0.000	0.000	0.001
xPredictROCR	0.001	0.000	0.001
xRWR	0.002	0.000	0.002
xSNP2cGenes	0.090	0.009	1.249
xSNP2eGenes	0.079	0.008	1.235
xSNPeqtl	0.101	0.011	1.260
xSNPhic	0.125	0.011	1.286

BioC 3.4: CHECK report for Pi on morelia

Summary

Command output