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CHECK report for GEM on machv2

This page was generated on 2020-10-17 11:58:31 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE GEM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 669/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GEM 1.14.0
Hong Pan
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/GEM
Branch: RELEASE_3_11
Last Commit: ea3bcca
Last Changed Date: 2020-04-27 14:58:10 -0400 (Mon, 27 Apr 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  WARNINGS  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: GEM
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GEM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GEM_1.14.0.tar.gz
StartedAt: 2020-10-17 01:23:01 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:24:42 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 100.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GEM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GEM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GEM_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GEM.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GEM’ 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 ‘GEM’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
GEM_GxEmodel 12.794   1.02  14.718
* 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: OK


Installation output

GEM.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GEM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘GEM’ ...
** using staged installation
** R
** 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 (GEM)

Tests output

GEM.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-apple-darwin17.0 (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("GEM")
100.00% done, 100 CpGs
Analysis done in:  0.052  seconds 
100.00% done, 144 methQTL
Analysis done in:  0.101  seconds 
100.00% done, 9 cpg-snp pairs
Analysis done in:  0.167  seconds 
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'
`geom_smooth()` using formula 'y ~ x'


RUNIT TEST PROTOCOL -- Sat Oct 17 01:24:26 2020 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GEM 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 
 15.256   1.364  17.376 

Example timings

GEM.Rcheck/GEM-Ex.timings

nameusersystemelapsed
GEM-package0.0000.0000.001
GEM_Emodel0.4480.0890.621
GEM_GUI0.0000.0010.000
GEM_GWASmodel0.5930.0680.751
GEM_Gmodel0.3610.0420.401
GEM_GxEmodel12.794 1.02014.718
SlicedData-class000