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CHECK report for CAnD on nebbiolo1

This page was generated on 2020-10-21 12:08:10 -0400 (Wed, 21 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CAnD PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 226/1939HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAnD 1.21.0
Caitlin McHugh
Snapshot Date: 2020-10-20 14:40:34 -0400 (Tue, 20 Oct 2020)
URL: https://git.bioconductor.org/packages/CAnD
Branch: master
Last Commit: 1cfd2da
Last Changed Date: 2020-04-27 14:48:46 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ OK ]
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  OK  OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAnD
Version: 1.21.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CAnD.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CAnD_1.21.0.tar.gz
StartedAt: 2020-10-20 20:11:00 -0400 (Tue, 20 Oct 2020)
EndedAt: 2020-10-20 20:11:45 -0400 (Tue, 20 Oct 2020)
EllapsedTime: 44.8 seconds
RetCode: 0
Status:  OK 
CheckDir: CAnD.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:CAnD.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings CAnD_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/CAnD.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 ‘CAnD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CAnD’ version ‘1.21.0’
* 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 ‘CAnD’ 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
CAnD : pairedTtest: no visible global function definition for ‘t.test’
barPlotAncest: no visible binding for global variable ‘id’
barPlotAncest: no visible binding for global variable ‘value’
barPlotAncest: no visible binding for global variable ‘variable’
calc_combP: no visible binding for global variable ‘var’
calc_combP: no visible global function definition for ‘pchisq’
plotPvals: no visible binding for global variable ‘numPs’
plotPvals: no visible binding for global variable ‘pval’
Undefined global functions or variables:
  id numPs pchisq pval t.test value var variable
Consider adding
  importFrom("stats", "pchisq", "t.test", "var")
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’ ... OK
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/CAnD.Rcheck/00check.log’
for details.



Installation output

CAnD.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL CAnD
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘CAnD’ ...
** 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 (CAnD)

Tests output

CAnD.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("CAnD")


RUNIT TEST PROTOCOL -- Tue Oct 20 20:11:24 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CAnD RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.009   0.076   1.070 

Example timings

CAnD.Rcheck/CAnD-Ex.timings

nameusersystemelapsed
BonfCorr-method0.0180.0090.026
CAnD0.0250.0000.024
CAnDResult-class0.0000.0010.001
barPlotAncest0.0010.0000.002
calc_combP0.0070.0040.011
overallStatistic-method0.0030.0040.007
overallpValue-method0.0030.0040.007
pValues-method0.0060.0030.009
plotPvals0.0200.0010.019
test-method0.0030.0030.007