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This page was generated on 2021-10-13 15:05:53 -0400 (Wed, 13 Oct 2021).

CHECK results for Glimma on machv2

To the developers/maintainers of the Glimma package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Glimma.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 774/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Glimma 2.2.0  (landing page)
Shian Su
Snapshot Date: 2021-10-12 04:50:13 -0400 (Tue, 12 Oct 2021)
git_url: https://git.bioconductor.org/packages/Glimma
git_branch: RELEASE_3_13
git_last_commit: 56d8c66
git_last_commit_date: 2021-05-19 12:19:39 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Glimma
Version: 2.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Glimma.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Glimma_2.2.0.tar.gz
StartedAt: 2021-10-12 19:33:00 -0400 (Tue, 12 Oct 2021)
EndedAt: 2021-10-12 19:41:25 -0400 (Tue, 12 Oct 2021)
EllapsedTime: 504.9 seconds
RetCode: 0
Status:   OK  
CheckDir: Glimma.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Glimma.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Glimma_2.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/Glimma.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Glimma/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Glimma’ version ‘2.2.0’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Glimma’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data          1.9Mb
    htmlwidgets   5.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
glimmaMA.DESeqDataSet      18.796  0.338  19.172
glimmaVolcano.DESeqDataSet 17.962  0.218  18.196
glMDPlot                   10.025  0.139  10.171
glimmaVolcano.DGEExact      7.933  0.233   8.171
glimmaMA.DGEExact           7.724  0.255   8.036
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/Glimma.Rcheck/00check.log’
for details.



Installation output

Glimma.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Glimma
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘Glimma’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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 (Glimma)

Tests output

Glimma.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)
> test_check("Glimma")
Loading required package: Glimma
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 191 ]
> 
> proc.time()
   user  system elapsed 
177.963   9.892 188.572 

Example timings

Glimma.Rcheck/Glimma-Ex.timings

nameusersystemelapsed
as.hexcol0.0020.0000.003
glMDPlot.MArrayLM000
glMDPlot10.025 0.13910.171
glMDRmd0.0010.0000.001
glMDSPlot0.0510.0040.055
glXYPlot0.0020.0010.002
glimmaMA.DESeqDataSet18.796 0.33819.172
glimmaMA.DGEExact7.7240.2558.036
glimmaMA.MArrayLM4.1250.1404.274
glimmaMA0.0180.0000.018
glimmaMDS.DESeqDataSet1.5680.0531.626
glimmaMDS.DGEList0.1560.0260.186
glimmaMDS0.9730.1111.088
glimmaMDS.default0.1580.0720.230
glimmaVolcano.DESeqDataSet17.962 0.21818.196
glimmaVolcano.DGEExact7.9330.2338.171
glimmaVolcano4.1730.1524.330
glimmaXY3.6360.1113.765