Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:18 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for DRIMSeq on nebbiolo2


To the developers/maintainers of the DRIMSeq package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DRIMSeq.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 541/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DRIMSeq 1.22.0  (landing page)
Malgorzata Nowicka
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/DRIMSeq
git_branch: RELEASE_3_14
git_last_commit: a22c59b
git_last_commit_date: 2021-10-26 12:26:21 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: DRIMSeq
Version: 1.22.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DRIMSeq.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DRIMSeq_1.22.0.tar.gz
StartedAt: 2022-04-12 07:15:12 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 07:18:24 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 192.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DRIMSeq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:DRIMSeq.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings DRIMSeq_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/DRIMSeq.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.22.0’
* 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 (user + system) or elapsed time > 5s
                   user system elapsed
dmSQTLtest-class 94.748  1.448  96.197
dmDStest-class    6.494  0.156   6.651
* 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-3.14-bioc/meat/DRIMSeq.Rcheck/00check.log’
for details.



Installation output

DRIMSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL DRIMSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘DRIMSeq’ ...
** using staged installation
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘proportions’ in package ‘DRIMSeq’
** 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)

Tests output

DRIMSeq.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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)

Attaching package: 'DRIMSeq'

The following object is masked from 'package:base':

    proportions

> 
> test_check("DRIMSeq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 21 ]
> 
> proc.time()
   user  system elapsed 
  6.256   0.376   6.617 

Example timings

DRIMSeq.Rcheck/DRIMSeq-Ex.timings

nameusersystemelapsed
dmDSdata-class0.0090.0000.009
dmDSdata0.0070.0000.006
dmDSfit-class0.0080.0000.008
dmDSprecision-class0.0070.0000.006
dmDStest-class6.4940.1566.651
dmFilter0.0240.0000.026
dmFit0.0080.0000.008
dmPrecision0.0070.0000.007
dmSQTLdata-class0.0060.0000.007
dmSQTLdata0.0070.0000.006
dmSQTLfit-class0.0070.0000.006
dmSQTLprecision-class0.0070.0000.006
dmSQTLtest-class94.748 1.44896.197
dmTest0.0050.0040.009
plotData0.0130.0000.012
plotPValues0.0060.0000.006
plotPrecision0.0050.0000.006
plotProportions0.0070.0000.007