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CHECK report for GENESIS on merida1

This page was generated on 2019-04-16 11:58:27 -0400 (Tue, 16 Apr 2019).

Package 609/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GENESIS 2.12.4
Stephanie M. Gogarten
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/GENESIS
Branch: RELEASE_3_8
Last Commit: 0b4d36e
Last Changed Date: 2019-02-20 14:45:04 -0400 (Wed, 20 Feb 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GENESIS
Version: 2.12.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GENESIS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GENESIS_2.12.4.tar.gz
StartedAt: 2019-04-16 00:10:09 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:16:12 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 363.3 seconds
RetCode: 0
Status:  OK 
CheckDir: GENESIS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GENESIS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GENESIS_2.12.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GENESIS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GENESIS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GENESIS’ version ‘2.12.4’
* 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 ‘GENESIS’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘survey:::saddle’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.pcrelate: no visible binding for global variable ‘k’
calcISAFBeta: no visible binding for global variable ‘k’
pcrelateSampBlock: no visible binding for global variable ‘k’
Undefined global functions or variables:
  k
* 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
Examples with CPU or elapsed time > 5s
               user system elapsed
fitNullModel 16.673  2.755  16.388
varCompCI    14.792  2.011  14.797
pcrelate     13.617  1.436  14.024
admixMap     12.484  0.627  13.333
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/GENESIS.Rcheck/00check.log’
for details.



Installation output

GENESIS.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GENESIS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘GENESIS’ ...
** 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
* DONE (GENESIS)

Tests output

GENESIS.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> library(testthat)
> library(GENESIS)
> 
> test_check("GENESIS")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 355 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
137.820  27.461 116.150 

Example timings

GENESIS.Rcheck/GENESIS-Ex.timings

nameusersystemelapsed
admixMap12.484 0.62713.333
admixMapMM0.0010.0000.001
assocTestAggregate3.2840.0443.358
assocTestMM0.0000.0010.001
assocTestSingle2.4630.2402.714
fitNullMM0.0000.0000.001
fitNullModel16.673 2.75516.388
kin2gds1.2040.8610.701
king2mat000
kingToMatrix1.7621.8770.695
pcair0.8470.6300.547
pcairPartition0.0850.0320.119
pcrelate13.617 1.43614.024
pcrelate_deprecated0.0020.0030.000
plot.pcair0.8380.6200.528
print.pcair0.5300.0540.592
varCompCI14.792 2.01114.797