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This page was generated on 2023-10-20 09:37:57 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Base 1.48.0  (landing page)
Laure Cougnaud
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/a4Base
git_branch: RELEASE_3_17
git_last_commit: 26d5793
git_last_commit_date: 2023-04-25 10:19:28 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for a4Base on kjohnson2


To the developers/maintainers of the a4Base package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: a4Base
Version: 1.48.0
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_1.48.0.tar.gz
StartedAt: 2023-10-17 01:05:12 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 01:10:51 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 339.7 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_1.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/a4Base.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.48.0’
* 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 startup messages can be suppressed ... 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
checkRd: (-1) filterVarInt.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) histPvalue.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) lassoReg.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) spectralMap.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) volcanoPlot.Rd:45: Escaped LaTeX specials: \&
* 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           10.186  0.412  16.214
computeLogRatio        5.245  0.203   7.328
plotLogRatio           4.692  0.125   7.358
plotCombination2genes  3.464  0.090   5.440
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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
a4palette0.0300.0030.047
addQuantilesColors1.8840.1823.115
boxPlot2.7950.0994.007
combineTwoExpressionSet000
computeLogRatio5.2450.2037.328
createExpressionSet0.0420.0010.062
filterVarInt1.8700.0752.843
heatmap.expressionSet0.0010.0010.002
histPvalue2.4520.0803.738
histpvalueplotter1.9080.0642.934
lassoReg1.9820.0683.088
logReg0.0000.0000.001
nlcvTT0.0010.0000.000
plot1gene1.8680.0632.876
plotComb2Samples2.0070.0883.126
plotCombMultSamples2.6790.1334.263
plotCombination2genes3.4640.0905.440
plotLogRatio4.6920.1257.358
probabilitiesPlot000
probe2gene1.6190.0532.556
profilesPlot1.9100.0683.035
propdegenescalculation1.9110.0693.033
replicates0.0010.0010.004
spectralMap10.186 0.41216.214
tTest2.1720.0903.445
volcanoPlot2.3620.0883.614