BioC 3.4: CHECK report for Pi on malbec1

Package: Pi

Version: 1.2.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Pi_1.2.1.tar.gz

StartedAt: 2017-04-15 00:24:52 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:29:16 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 264.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Pi.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Pi_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Pi.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘/home/biocbuild/bbs-3.4-bioc/meat/Pi.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
* 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
  ‘/home/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	0.016	0.004	0.019
xGSsimulator	0.004	0.000	0.001
xMLdensity	0	0	0
xMLdotplot	0	0	0
xMLrandomforest	0.004	0.000	0.001
xPCHiCplot	0.092	0.000	1.027
xPier	0.000	0.000	0.001
xPierGenes	0.104	0.000	0.877
xPierManhattan	0.176	0.008	1.024
xPierMatrix	0	0	0
xPierPathways	0.096	0.004	0.869
xPierSNPs	0.144	0.004	1.184
xPierSNPsAdv	0.148	0.000	0.918
xPierSNPsConsensus	0.152	0.000	0.917
xPierSubnet	0.144	0.004	0.916
xPierTrack	0.144	0.008	0.922
xPredictCompare	0.000	0.000	0.001
xPredictROCR	0.000	0.000	0.001
xRWR	0.000	0.004	0.003
xSNP2cGenes	0.104	0.004	0.879
xSNP2eGenes	0.148	0.004	0.921
xSNPeqtl	0.092	0.008	0.835
xSNPhic	0.148	0.004	0.892