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) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:58:27 -0400 (Tue, 16 Apr 2019).
| Package 609/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GENESIS 2.12.4 Stephanie M. Gogarten
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| 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 |
##############################################################################
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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.
GENESIS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GENESIS ### ############################################################################## ############################################################################## * 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)
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
GENESIS.Rcheck/GENESIS-Ex.timings
| name | user | system | elapsed | |
| admixMap | 12.484 | 0.627 | 13.333 | |
| admixMapMM | 0.001 | 0.000 | 0.001 | |
| assocTestAggregate | 3.284 | 0.044 | 3.358 | |
| assocTestMM | 0.000 | 0.001 | 0.001 | |
| assocTestSingle | 2.463 | 0.240 | 2.714 | |
| fitNullMM | 0.000 | 0.000 | 0.001 | |
| fitNullModel | 16.673 | 2.755 | 16.388 | |
| kin2gds | 1.204 | 0.861 | 0.701 | |
| king2mat | 0 | 0 | 0 | |
| kingToMatrix | 1.762 | 1.877 | 0.695 | |
| pcair | 0.847 | 0.630 | 0.547 | |
| pcairPartition | 0.085 | 0.032 | 0.119 | |
| pcrelate | 13.617 | 1.436 | 14.024 | |
| pcrelate_deprecated | 0.002 | 0.003 | 0.000 | |
| plot.pcair | 0.838 | 0.620 | 0.528 | |
| print.pcair | 0.530 | 0.054 | 0.592 | |
| varCompCI | 14.792 | 2.011 | 14.797 | |