Package: DRIMSeq

Version: 1.14.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DRIMSeq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DRIMSeq_1.14.0.tar.gz

StartedAt: 2020-04-15 03:39:58 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:44:59 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 301.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: DRIMSeq.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DRIMSeq.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DRIMSeq_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/DRIMSeq.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DRIMSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DRIMSeq’ 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 ‘DRIMSeq’ 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 ... WARNING
Documented arguments not in \usage in documentation object 'dmSQTLtest-class':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
dmSQTLtest-class 172.892  1.744 175.062
dmDStest-class    11.704  0.112  11.956
* 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: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/DRIMSeq.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL DRIMSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘DRIMSeq’ ...
** using staged installation
** R
** inst
** preparing 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 (DRIMSeq)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(DRIMSeq)
> 
> test_check("DRIMSeq")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 21 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  8.684   0.232   8.929 

name	user	system	elapsed
dmDSdata-class	0.008	0.004	0.022
dmDSdata	0.008	0.000	0.009
dmDSfit-class	0.012	0.000	0.009
dmDSprecision-class	0.008	0.000	0.009
dmDStest-class	11.704	0.112	11.956
dmFilter	0.032	0.000	0.097
dmFit	0.012	0.000	0.011
dmPrecision	0.012	0.000	0.010
dmSQTLdata-class	0.012	0.000	0.010
dmSQTLdata	0.012	0.000	0.012
dmSQTLfit-class	0.012	0.000	0.012
dmSQTLprecision-class	0.012	0.000	0.012
dmSQTLtest-class	172.892	1.744	175.062
dmTest	0.016	0.000	0.012
plotData	0.020	0.000	0.021
plotPValues	0.008	0.000	0.006
plotPrecision	0.004	0.004	0.006
plotProportions	0.008	0.000	0.006