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This page was generated on 2021-09-27 15:05:59 -0400 (Mon, 27 Sep 2021).

CHECK results for GENESIS on nebbiolo1

To the developers/maintainers of the GENESIS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GENESIS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 726/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GENESIS 2.22.2  (landing page)
Stephanie M. Gogarten
Snapshot Date: 2021-09-26 04:50:10 -0400 (Sun, 26 Sep 2021)
git_url: https://git.bioconductor.org/packages/GENESIS
git_branch: RELEASE_3_13
git_last_commit: df77222
git_last_commit_date: 2021-06-16 02:13:52 -0400 (Wed, 16 Jun 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GENESIS
Version: 2.22.2
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GENESIS.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GENESIS_2.22.2.tar.gz
StartedAt: 2021-09-26 09:56:50 -0400 (Sun, 26 Sep 2021)
EndedAt: 2021-09-26 10:01:29 -0400 (Sun, 26 Sep 2021)
EllapsedTime: 278.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GENESIS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GENESIS.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GENESIS_2.22.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/GENESIS.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘2.22.2’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
fitNullModel 17.578  0.620  18.064
varCompCI    13.853  0.348  14.092
pcrelate     12.295  0.257  12.433
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/GENESIS.Rcheck/00check.log’
for details.



Installation output

GENESIS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL GENESIS
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘GENESIS’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c fht.c -o fht.o
gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o GENESIS.so fht.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-GENESIS/00new/GENESIS/libs
** 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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GENESIS)

Tests output

GENESIS.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
# of selected variants: 10
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 623 ]
> 
> proc.time()
   user  system elapsed 
 83.992   1.713  83.989 

Example timings

GENESIS.Rcheck/GENESIS-Ex.timings

nameusersystemelapsed
admixMap0.4780.0500.528
assocTestAggregate3.4090.1213.529
assocTestSingle2.6340.1042.738
computeVSIF0.0650.0000.065
effectAllele1.0530.0681.096
fitNullModel17.578 0.62018.064
jointScoreTest0.0540.0080.062
kin2gds0.4530.0110.446
kingToMatrix0.4260.0040.381
pcair0.3250.0170.342
pcairPartition0.0240.0030.027
pcrelate12.295 0.25712.433
plot.pcair0.3390.0120.353
print.pcair0.3260.0140.340
varCompCI13.853 0.34814.092