Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-01 17:18:10 -0500 (Wed, 01 Dec 2021).

CHECK results for a4Base on machv2

To the developers/maintainers of the a4Base package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/a4Base.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 2/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Base 1.42.0  (landing page)
Laure Cougnaud
Snapshot Date: 2021-11-30 04:15:05 -0500 (Tue, 30 Nov 2021)
git_url: https://git.bioconductor.org/packages/a4Base
git_branch: RELEASE_3_14
git_last_commit: d7296e2
git_last_commit_date: 2021-10-26 11:58:47 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: a4Base
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:a4Base.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings a4Base_1.42.0.tar.gz
StartedAt: 2021-11-30 13:32:07 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 13:36:26 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 258.5 seconds
RetCode: 0
Status:   OK  
CheckDir: a4Base.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:a4Base.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings a4Base_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/a4Base.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.42.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘JavaGD’
* 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 ‘a4Base’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
spectralMap     11.356  0.445  11.825
plotLogRatio     7.773  0.117   7.914
computeLogRatio  7.111  0.189   7.312
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/a4Base.Rcheck/00check.log’
for details.



Installation output

a4Base.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL a4Base
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘a4Base’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (a4Base)

Tests output


Example timings

a4Base.Rcheck/a4Base-Ex.timings

nameusersystemelapsed
a4palette0.0370.0020.039
addQuantilesColors2.2560.2462.505
boxPlot3.0290.0693.104
combineTwoExpressionSet000
computeLogRatio7.1110.1897.312
createExpressionSet0.040.000.04
filterVarInt2.3790.0882.471
heatmap.expressionSet0.0010.0030.004
histPvalue2.7650.0792.847
histpvalueplotter2.3380.0462.390
lassoReg2.4340.0432.479
logReg0.0000.0010.001
nlcvTT0.0000.0000.001
plot1gene2.3330.0572.400
plotComb2Samples2.5150.0722.590
plotCombMultSamples3.2690.1473.456
plotCombination2genes3.0760.0723.174
plotLogRatio7.7730.1177.914
probabilitiesPlot0.0000.0000.001
probe2gene2.1560.0362.194
profilesPlot2.3480.0392.389
propdegenescalculation2.3780.0532.432
replicates0.0020.0000.002
spectralMap11.356 0.44511.825
tTest2.4720.0802.556
volcanoPlot2.8530.0752.931