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CHECK report for hierGWAS on nebbiolo1

This page was generated on 2021-01-19 11:53:37 -0500 (Tue, 19 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE hierGWAS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 832/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hierGWAS 1.20.0
Laura Buzdugan
Snapshot Date: 2021-01-18 14:42:24 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/hierGWAS
Branch: RELEASE_3_12
Last Commit: 1559099
Last Changed Date: 2020-10-27 11:05:51 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.5 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
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hierGWAS
Version: 1.20.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:hierGWAS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings hierGWAS_1.20.0.tar.gz
StartedAt: 2021-01-18 21:47:07 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 21:48:24 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 76.1 seconds
RetCode: 0
Status:  OK 
CheckDir: hierGWAS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:hierGWAS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings hierGWAS_1.20.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/hierGWAS.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 ‘hierGWAS/DESCRIPTION’ ... OK
* this is package ‘hierGWAS’ version ‘1.20.0’
* 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 ‘hierGWAS’ 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
MEL: no visible global function definition for ‘glm’
MEL: no visible binding for global variable ‘binomial’
MEL: no visible global function definition for ‘glm.control’
MEL: no visible global function definition for ‘coef’
adj.pval: no visible global function definition for ‘quantile’
cluster.snp: no visible global function definition for ‘cor’
cluster.snp: no visible global function definition for ‘as.dist’
cluster.snp: no visible global function definition for ‘as.dendrogram’
return.r2: no visible global function definition for ‘lm’
test.hierarchy: no visible global function definition for
  ‘order.dendrogram’
test.snp: no visible global function definition for ‘anova’
test.snp: no visible global function definition for ‘lm’
Undefined global functions or variables:
  anova as.dendrogram as.dist binomial coef cor glm glm.control lm
  order.dendrogram quantile
Consider adding
  importFrom("stats", "anova", "as.dendrogram", "as.dist", "binomial",
             "coef", "cor", "glm", "glm.control", "lm",
             "order.dendrogram", "quantile")
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/hierGWAS.Rcheck/00check.log’
for details.



Installation output

hierGWAS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL hierGWAS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘hierGWAS’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (hierGWAS)

Tests output

hierGWAS.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("hierGWAS")


RUNIT TEST PROTOCOL -- Mon Jan 18 21:47:47 2021 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
hierGWAS RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.671   0.143   1.798 

Example timings

hierGWAS.Rcheck/hierGWAS-Ex.timings

nameusersystemelapsed
cluster.snp0.0190.0080.028
compute.r20.2920.0360.328
multisplit0.4060.0040.410
simGWAS0.0030.0000.003
test.hierarchy2.6250.0042.628