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CHECK report for DRIMSeq on tokay2

This page was generated on 2020-10-17 11:56:29 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE DRIMSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 504/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DRIMSeq 1.16.1
Malgorzata Nowicka
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/DRIMSeq
Branch: RELEASE_3_11
Last Commit: 7225753
Last Changed Date: 2020-08-05 08:21:37 -0400 (Wed, 05 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: DRIMSeq
Version: 1.16.1
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DRIMSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DRIMSeq_1.16.1.tar.gz
StartedAt: 2020-10-17 03:32:59 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:41:54 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 534.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: DRIMSeq.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DRIMSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DRIMSeq_1.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/DRIMSeq.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.16.1'
* 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 ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpusFIQt/R.INSTALL21dc1e7c472e/DRIMSeq/man/dmTest.Rd:93: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpusFIQt/R.INSTALL21dc1e7c472e/DRIMSeq/man/dmTest.Rd:193: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/DRIMSeq.Rcheck/00install.out' for details.
* 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 168.61   0.30  168.96
dmDStest-class    10.34   0.11   10.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
dmSQTLtest-class 171.60   0.19  171.80
dmDStest-class    12.38   0.08   12.46
* 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: 2 WARNINGs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/DRIMSeq.Rcheck/00check.log'
for details.



Installation output

DRIMSeq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/DRIMSeq_1.16.1.tar.gz && rm -rf DRIMSeq.buildbin-libdir && mkdir DRIMSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DRIMSeq.buildbin-libdir DRIMSeq_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DRIMSeq_1.16.1.zip && rm DRIMSeq_1.16.1.tar.gz DRIMSeq_1.16.1.zip
###
##############################################################################
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  % 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 83962  100 83962    0     0  1455k      0 --:--:-- --:--:-- --:--:-- 1673k

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  
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpusFIQt/R.INSTALL21dc1e7c472e/DRIMSeq/man/dmTest.Rd:93: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpusFIQt/R.INSTALL21dc1e7c472e/DRIMSeq/man/dmTest.Rd:193: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
    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_1.16.1.zip
* DONE (DRIMSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'DRIMSeq' successfully unpacked and MD5 sums checked

Tests output

DRIMSeq.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 21 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  11.73    0.42   12.14 

DRIMSeq.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 21 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   8.92    0.32    9.23 

Example timings

DRIMSeq.Rcheck/examples_i386/DRIMSeq-Ex.timings

nameusersystemelapsed
dmDSdata-class0.020.000.01
dmDSdata0.010.000.02
dmDSfit-class000
dmDSprecision-class000
dmDStest-class10.34 0.1110.53
dmFilter0.030.000.11
dmFit0.020.000.01
dmPrecision0.010.000.02
dmSQTLdata-class0.020.000.02
dmSQTLdata0.010.000.01
dmSQTLfit-class0.020.000.02
dmSQTLprecision-class0.010.000.01
dmSQTLtest-class168.61 0.30168.96
dmTest0.000.020.01
plotData0.020.010.03
plotPValues0.010.000.02
plotPrecision0.020.000.01
plotProportions0.000.020.02

DRIMSeq.Rcheck/examples_x64/DRIMSeq-Ex.timings

nameusersystemelapsed
dmDSdata-class0.020.000.01
dmDSdata000
dmDSfit-class000
dmDSprecision-class0.000.010.01
dmDStest-class12.38 0.0812.46
dmFilter0.000.020.01
dmFit0.000.010.02
dmPrecision0.010.000.01
dmSQTLdata-class0.000.020.02
dmSQTLdata0.020.000.01
dmSQTLfit-class0.010.000.02
dmSQTLprecision-class000
dmSQTLtest-class171.60 0.19171.80
dmTest0.010.000.01
plotData0.020.010.04
plotPValues0.020.000.02
plotPrecision0.020.000.01
plotProportions0.010.000.02