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CHECK report for GeneOverlap on malbec1

This page was generated on 2018-04-12 13:11:48 -0400 (Thu, 12 Apr 2018).

Package 541/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneOverlap 1.14.0
Li Shen, Mount Sinai
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GeneOverlap
Branch: RELEASE_3_6
Last Commit: e8dd1e4
Last Changed Date: 2017-10-30 12:40:10 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneOverlap
Version: 1.14.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GeneOverlap_1.14.0.tar.gz
StartedAt: 2018-04-11 23:45:22 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:45:47 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 24.7 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneOverlap.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings GeneOverlap_1.14.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/GeneOverlap.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneOverlap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneOverlap’ version ‘1.14.0’
* 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 ‘GeneOverlap’ can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
drawHeatmap,GeneOverlapMatrix: no visible global function definition
  for ‘p.adjust’
print,GeneOverlap: no visible global function definition for ‘head’
testGeneOverlap,GeneOverlap: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  head p.adjust setNames
Consider adding
  importFrom("stats", "p.adjust", "setNames")
  importFrom("utils", "head")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files look like leftovers/mistakes:
  ‘Rplots.pdf’
Please remove them from your package.
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/GeneOverlap.Rcheck/00check.log’
for details.



Installation output

GeneOverlap.Rcheck/00install.out

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

Tests output

GeneOverlap.Rcheck/tests/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("GeneOverlap")


RUNIT TEST PROTOCOL -- Wed Apr 11 23:45:44 2018 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GeneOverlap RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In getPval(go.obj) : Test has not been performed yet.

2: In getOddsRatio(go.obj) : Test has not been performed yet.

> 
> proc.time()
   user  system elapsed 
  0.716   0.036   0.746 

Example timings

GeneOverlap.Rcheck/GeneOverlap-Ex.timings

nameusersystemelapsed
GeneOverlap0.0880.0120.098
GeneOverlapMatrix0.2560.0000.254
drawHeatmap1.1520.0041.158
getGenomeSize0.0680.0000.068
getList0.0360.0000.036
getReadonly0.0360.0000.034
getReadonlyMatrix0.1720.0000.172
gs.RNASeq0.0240.0000.024
hESC.ChIPSeq.list0.0320.0000.033
hESC.RNASeq.list0.0320.0000.031
newGOM0.1440.0000.145
newGeneOverlap0.0480.0000.049
testGeneOverlap0.0360.0000.036