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This page was generated on 2025-08-28 12:04 -0400 (Thu, 28 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4822
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4613
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4556
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
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 2/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Base 1.57.0  (landing page)
Laure Cougnaud
Snapshot Date: 2025-08-27 13:45 -0400 (Wed, 27 Aug 2025)
git_url: https://git.bioconductor.org/packages/a4Base
git_branch: devel
git_last_commit: a598984
git_last_commit_date: 2025-04-15 10:07:51 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for a4Base on lconway

To the developers/maintainers of the a4Base package:
- 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 Troubleshooting Build Report for more information.
- 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: 1.57.0
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_1.57.0.tar.gz
StartedAt: 2025-08-27 19:01:01 -0400 (Wed, 27 Aug 2025)
EndedAt: 2025-08-27 19:04:39 -0400 (Wed, 27 Aug 2025)
EllapsedTime: 218.6 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_1.57.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/a4Base.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.57.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
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 code 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 whether 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) computeLogRatio.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeLogRatio.Rd:52-55: Lost braces in \itemize; meant \describe ?
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) plotLogRatio.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLogRatio.Rd:167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLogRatio.Rd:168: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLogRatio.Rd:169: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLogRatio.Rd:170: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLogRatio.Rd:183-185: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLogRatio.Rd:186-191: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLogRatio.Rd:192-200: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotLogRatio.Rd:201-203: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spectralMap.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) topTable-methods.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) volcanoPlot.Rd:45: Escaped LaTeX specials: \&
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'a4palette.Rd':
  ‘[grDevices]{palettes}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ExpressionSetWithComputation-class.Rd: ExpressionSet-class,
    eSet-class, VersionedBiobase-class, Versioned-class
  combineTwoExpressionSet.Rd: ExpressionSet-class
  createExpressionSet.Rd: ExpressionSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 10.213  0.471   10.77
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-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
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘a4Base’ ...
** this is package ‘a4Base’ version ‘1.57.0’
** 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
a4palette0.0460.0020.049
addQuantilesColors1.4340.1831.631
boxPlot2.3200.0792.418
combineTwoExpressionSet000
computeLogRatio4.3820.1824.601
createExpressionSet0.0340.0010.035
filterVarInt1.9740.0872.080
heatmap.expressionSet0.0010.0020.002
histPvalue1.3630.0461.419
histpvalueplotter1.3720.0531.440
lassoReg1.4170.0491.479
logReg000
nlcvTT0.0000.0010.000
plot1gene1.3590.0531.429
plotComb2Samples1.5090.0791.604
plotCombMultSamples2.5990.1352.758
plotCombination2genes2.3190.0552.392
plotLogRatio3.9990.1324.174
probabilitiesPlot0.0000.0010.000
probe2gene1.0530.0351.097
profilesPlot1.3290.0491.399
propdegenescalculation1.9050.0732.002
replicates0.0020.0000.002
spectralMap10.213 0.47110.770
tTest1.7250.0761.822
volcanoPlot1.8880.0992.007