Back to Multiple platform build/check report for BioC 3.13
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-09-20 15:05:11 -0400 (Mon, 20 Sep 2021).

CHECK results for DRIMSeq on tokay2

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? 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 532/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DRIMSeq 1.20.0  (landing page)
Malgorzata Nowicka
Snapshot Date: 2021-09-19 04:50:10 -0400 (Sun, 19 Sep 2021)
git_url: https://git.bioconductor.org/packages/DRIMSeq
git_branch: RELEASE_3_13
git_last_commit: 27f2619
git_last_commit_date: 2021-05-19 12:18:54 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.20.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DRIMSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DRIMSeq_1.20.0.tar.gz
StartedAt: 2021-09-19 21:53:21 -0400 (Sun, 19 Sep 2021)
EndedAt: 2021-09-19 22:01:18 -0400 (Sun, 19 Sep 2021)
EllapsedTime: 477.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DRIMSeq.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DRIMSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DRIMSeq_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DRIMSeq.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DRIMSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DRIMSeq' version '1.20.0'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
dmSQTLtest-class 140.57   0.06  140.63
dmDStest-class    17.36   0.17   17.59
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
dmSQTLtest-class 142.27   0.13  142.39
dmDStest-class    18.14   0.09   18.23
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/DRIMSeq.Rcheck/00check.log'
for details.



Installation output

DRIMSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/DRIMSeq_1.20.0.tar.gz && rm -rf DRIMSeq.buildbin-libdir && mkdir DRIMSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DRIMSeq.buildbin-libdir DRIMSeq_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DRIMSeq_1.20.0.zip && rm DRIMSeq_1.20.0.tar.gz DRIMSeq_1.20.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 84255  100 84255    0     0   189k      0 --:--:-- --:--:-- --:--:--  190k

install for i386

* 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
  converting help for package 'DRIMSeq'
    finding HTML links ... done
    MatrixList-class                        html  
    dmDSdata-class                          html  
    dmDSdata                                html  
    dmDSfit-class                           html  
    dmDSprecision-class                     html  
    dmDStest-class                          html  
    dmFilter                                html  
    dmFit                                   html  
    finding level-2 HTML links ... done

    dmPrecision                             html  
    dmSQTLdata-class                        html  
    dmSQTLdata                              html  
    dmSQTLfit-class                         html  
    dmSQTLprecision-class                   html  
    dmSQTLtest-class                        html  
    dmTest                                  html  
    dm_plotDataDSInfo                       html  
    dm_plotProportions                      html  
    plotData                                html  
    plotPValues                             html  
    plotPrecision                           html  
    plotProportions                         html  
** 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

install for x64

* installing *source* package 'DRIMSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DRIMSeq' as DRIMSeq_1.20.0.zip
* DONE (DRIMSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'DRIMSeq' successfully unpacked and MD5 sums checked

Tests output

DRIMSeq.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  11.96    0.39   12.34 

DRIMSeq.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 
  11.20    0.23   11.40 

Example timings

DRIMSeq.Rcheck/examples_i386/DRIMSeq-Ex.timings

nameusersystemelapsed
dmDSdata-class0.020.000.01
dmDSdata000
dmDSfit-class0.010.000.01
dmDSprecision-class000
dmDStest-class17.36 0.1717.59
dmFilter0.010.000.44
dmFit0.020.000.02
dmPrecision0.000.020.01
dmSQTLdata-class0.010.000.02
dmSQTLdata0.000.010.01
dmSQTLfit-class0.020.000.02
dmSQTLprecision-class0.010.000.01
dmSQTLtest-class140.57 0.06140.63
dmTest0.010.000.02
plotData0.020.000.01
plotPValues000
plotPrecision0.010.000.02
plotProportions000

DRIMSeq.Rcheck/examples_x64/DRIMSeq-Ex.timings

nameusersystemelapsed
dmDSdata-class0.010.000.01
dmDSdata000
dmDSfit-class0.010.000.02
dmDSprecision-class0.020.000.02
dmDStest-class18.14 0.0918.23
dmFilter0.020.000.02
dmFit0.010.000.01
dmPrecision000
dmSQTLdata-class0.020.000.02
dmSQTLdata000
dmSQTLfit-class0.010.000.01
dmSQTLprecision-class000
dmSQTLtest-class142.27 0.13142.39
dmTest0.010.000.02
plotData000
plotPValues000
plotPrecision000
plotProportions0.020.000.02