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BioC 3.4: CHECK report for Pi on malbec1

This page was generated on 2017-04-15 16:14:06 -0400 (Sat, 15 Apr 2017).

Package 920/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Pi 1.2.1
Hai Fang
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/Pi
Last Changed Rev: 126727 / Revision: 128728
Last Changed Date: 2017-02-13 07:48:50 -0500 (Mon, 13 Feb 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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


* 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.


Pi.Rcheck/00install.out:

* 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)

Pi.Rcheck/Pi-Ex.timings:

nameusersystemelapsed
xContour0.0160.0040.019
xGSsimulator0.0040.0000.001
xMLdensity000
xMLdotplot000
xMLrandomforest0.0040.0000.001
xPCHiCplot0.0920.0001.027
xPier0.0000.0000.001
xPierGenes0.1040.0000.877
xPierManhattan0.1760.0081.024
xPierMatrix000
xPierPathways0.0960.0040.869
xPierSNPs0.1440.0041.184
xPierSNPsAdv0.1480.0000.918
xPierSNPsConsensus0.1520.0000.917
xPierSubnet0.1440.0040.916
xPierTrack0.1440.0080.922
xPredictCompare0.0000.0000.001
xPredictROCR0.0000.0000.001
xRWR0.0000.0040.003
xSNP2cGenes0.1040.0040.879
xSNP2eGenes0.1480.0040.921
xSNPeqtl0.0920.0080.835
xSNPhic0.1480.0040.892