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CHECK report for made4 on merida1

This page was generated on 2021-05-06 12:35:33 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the made4 package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 988/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
made4 1.64.0  (landing page)
Aedin Culhane
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/made4
Branch: RELEASE_3_12
Last Commit: 89d0a81
Last Changed Date: 2020-10-27 10:25:28 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: made4
Version: 1.64.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:made4.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings made4_1.64.0.tar.gz
StartedAt: 2021-05-06 03:14:36 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:17:35 -0400 (Thu, 06 May 2021)
EllapsedTime: 179.7 seconds
RetCode: 0
Status:   OK  
CheckDir: made4.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:made4.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings made4_1.64.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/made4.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘made4/DESCRIPTION’ ... OK
* this is package ‘made4’ version ‘1.64.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘made4’ 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 ... NOTE
prepare_Rd: asDataFrame.Rd:30: Dropping empty section \examples
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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-3.12-bioc/meat/made4.Rcheck/00check.log’
for details.



Installation output

made4.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL made4
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘made4’ ...
** 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 (made4)

Tests output


Example timings

made4.Rcheck/made4-Ex.timings

nameusersystemelapsed
NCI600.0060.0020.008
bet.coinertia0.0100.0010.010
between.graph0.3720.0450.417
bga0.4290.0190.450
bga.jackknife1.7260.0341.761
bga.suppl0.4500.0100.461
cia0.1940.0090.204
commonMap0.0290.0010.031
comparelists0.0000.0000.001
do3d0.4190.0100.431
genes1d0.1080.0100.117
getcol0.0290.0020.031
graph1D0.0760.0040.081
heatplot1.6810.0771.769
html3D0.6370.0130.652
isDataFrame0.0160.0020.020
khan0.0070.0020.008
ord0.2280.0130.277
overview0.1410.0100.151
plotarrays0.3120.0090.322
plotgenes0.1240.0050.129
prettyDend0.1020.0060.109
randomiser0.0030.0000.004
s.var0.2750.0110.288
sumstats0.2560.0050.262
suppl0.5170.0170.536
topgenes0.0930.0070.100