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CHECK report for GeneOverlap on malbec2

This page was generated on 2020-10-17 11:54:50 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE GeneOverlap PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 685/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneOverlap 1.24.0
Li Shen, Mount Sinai
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/GeneOverlap
Branch: RELEASE_3_11
Last Commit: d6b1170
Last Changed Date: 2020-06-20 14:49:54 -0400 (Sat, 20 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneOverlap
Version: 1.24.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GeneOverlap.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GeneOverlap_1.24.0.tar.gz
StartedAt: 2020-10-17 01:37:20 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:37:46 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 25.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneOverlap.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GeneOverlap.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GeneOverlap_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/GeneOverlap.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.24.0’
* 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 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 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-3.11-bioc/meat/GeneOverlap.Rcheck/00check.log’
for details.



Installation output

GeneOverlap.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL GeneOverlap
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘GeneOverlap’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GeneOverlap)

Tests output

GeneOverlap.Rcheck/tests/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 -- Sat Oct 17 01:37:43 2020 
*********************************************** 
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 
  0.681   0.070   0.747 

Example timings

GeneOverlap.Rcheck/GeneOverlap-Ex.timings

nameusersystemelapsed
GeneOverlap0.0620.0000.062
GeneOverlapMatrix0.2070.0240.230
drawHeatmap0.0900.0000.089
getGenomeSize0.0620.0000.062
getList0.0470.0000.048
getReadonly0.0400.0040.043
getReadonlyMatrix0.2410.0000.240
gs.RNASeq0.0310.0030.034
hESC.ChIPSeq.list0.0470.0000.046
hESC.RNASeq.list0.0490.0000.048
newGOM0.1620.0040.166
newGeneOverlap0.0250.0040.028
testGeneOverlap0.0330.0000.033