Package: GENESIS

Version: 2.12.4

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GENESIS.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GENESIS_2.12.4.tar.gz

StartedAt: 2019-04-16 00:09:43 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:15:14 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 332.0 seconds

RetCode: 0

Status:  OK

CheckDir: GENESIS.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GENESIS.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GENESIS_2.12.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/GENESIS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 17.624  0.184  14.834
pcrelate     16.996  0.064  14.267
varCompCI    16.456  0.060  13.492
admixMap     10.588  0.260  10.878
kingToMatrix  7.700  0.016   1.658
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/GENESIS.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL GENESIS
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

> library(testthat)
> library(GENESIS)
> 
> test_check("GENESIS")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 354 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
218.584   0.864 114.937 

name	user	system	elapsed
admixMap	10.588	0.260	10.878
admixMapMM	0	0	0
assocTestAggregate	2.920	0.004	2.952
assocTestMM	0	0	0
assocTestSingle	1.820	0.056	1.877
fitNullMM	0.004	0.000	0.000
fitNullModel	17.624	0.184	14.834
kin2gds	1.536	0.012	0.892
king2mat	0	0	0
kingToMatrix	7.700	0.016	1.658
pcair	0.504	0.008	0.513
pcairPartition	0.044	0.000	0.046
pcrelate	16.996	0.064	14.267
pcrelate_deprecated	0.000	0.000	0.001
plot.pcair	0.568	0.004	0.573
print.pcair	0.564	0.004	0.569
varCompCI	16.456	0.060	13.492