Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2023-02-01 11:06:51 -0500 (Wed, 01 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4511
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4289
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4318
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 palomino4


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 570/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DRIMSeq 1.26.0  (landing page)
Malgorzata Nowicka
Snapshot Date: 2023-01-31 14:00:04 -0500 (Tue, 31 Jan 2023)
git_url: https://git.bioconductor.org/packages/DRIMSeq
git_branch: RELEASE_3_16
git_last_commit: 69cf942
git_last_commit_date: 2022-11-01 11:13:16 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: DRIMSeq
Version: 1.26.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DRIMSeq.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings DRIMSeq_1.26.0.tar.gz
StartedAt: 2023-02-01 01:06:42 -0500 (Wed, 01 Feb 2023)
EndedAt: 2023-02-01 01:10:24 -0500 (Wed, 01 Feb 2023)
EllapsedTime: 222.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DRIMSeq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DRIMSeq.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings DRIMSeq_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/DRIMSeq.Rcheck'
* using R version 4.2.2 (2022-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.26.0'
* 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
dmSQTLtest-class 101.07   0.65  101.75
dmDStest-class     7.04   0.09    7.15
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/DRIMSeq.Rcheck/00check.log'
for details.



Installation output

DRIMSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL DRIMSeq
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-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 4.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   8.29    0.29    8.56 

Example timings

DRIMSeq.Rcheck/DRIMSeq-Ex.timings

nameusersystemelapsed
dmDSdata-class0.030.000.03
dmDSdata000
dmDSfit-class000
dmDSprecision-class000
dmDStest-class7.040.097.15
dmFilter0.030.000.06
dmFit000
dmPrecision0.020.000.02
dmSQTLdata-class0.020.000.01
dmSQTLdata000
dmSQTLfit-class0.010.000.02
dmSQTLprecision-class0.020.000.01
dmSQTLtest-class101.07 0.65101.75
dmTest0.000.020.02
plotData0.020.000.03
plotPValues000
plotPrecision0.010.000.01
plotProportions000