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CHECK report for Glimma on celaya2

This page was generated on 2020-01-16 13:45:01 -0500 (Thu, 16 Jan 2020).

Package 708/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Glimma 1.15.1
Shian Su
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/Glimma
Branch: master
Last Commit: 8e3d971
Last Changed Date: 2020-01-06 19:55:09 -0500 (Mon, 06 Jan 2020)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Glimma
Version: 1.15.1
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_1.15.1.tar.gz
StartedAt: 2020-01-16 04:59:27 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 05:01:35 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 128.0 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_1.15.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Glimma.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.15.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .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 ... 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 ... 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 data for ASCII and uncompressed saves ... 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
glMDPlot 14.575  0.372  15.239
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
> library(Glimma)
> 
> test_check("Glimma")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 143 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 28.415   3.070  31.576 

Example timings

Glimma.Rcheck/Glimma-Ex.timings

nameusersystemelapsed
as.hexcol0.0040.0000.005
glBar0.1030.0070.114
glBar.default0.0040.0030.007
glMDPlot.MArrayLM000
glMDPlot14.575 0.37215.239
glMDRmd0.0010.0000.001
glMDSPlot0.0820.0160.098
glScatter0.0030.0020.004
glScatter.default0.0030.0020.005
glXYPlot0.0030.0020.005
glimma0.0030.0030.005
gllink0.0040.0020.007