Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-25 11:35:01 -0400 (Sat, 25 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4516
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 2/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Base 1.52.0  (landing page)
Laure Cougnaud
Snapshot Date: 2024-05-24 14:00:07 -0400 (Fri, 24 May 2024)
git_url: https://git.bioconductor.org/packages/a4Base
git_branch: RELEASE_3_19
git_last_commit: 7312ef9
git_last_commit_date: 2024-04-30 10:24:08 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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 13.6.5 Ventura / arm64see weekly results here

CHECK results for a4Base on nebbiolo1


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: 1.52.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:a4Base.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings a4Base_1.52.0.tar.gz
StartedAt: 2024-05-24 19:59:27 -0400 (Fri, 24 May 2024)
EndedAt: 2024-05-24 20:02:35 -0400 (Fri, 24 May 2024)
EllapsedTime: 187.0 seconds
RetCode: 0
Status:   OK  
CheckDir: a4Base.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:a4Base.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings a4Base_1.52.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/a4Base.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.52.0’
* 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 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 loading without being on the library search path ... 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 ... 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 9.535  0.316   9.851
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/a4Base.Rcheck/00check.log’
for details.


Installation output

a4Base.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL a4Base
###
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##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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
a4palette0.0440.0000.044
addQuantilesColors1.7720.1761.948
boxPlot2.5810.1002.680
combineTwoExpressionSet000
computeLogRatio4.2770.2804.557
createExpressionSet0.0310.0000.031
filterVarInt2.1940.1122.306
heatmap.expressionSet0.0020.0000.002
histPvalue1.7090.0441.753
histpvalueplotter1.6970.0641.760
lassoReg1.7880.0531.841
logReg0.0000.0000.001
nlcvTT0.0000.0000.001
plot1gene1.6860.0431.729
plotComb2Samples1.8900.0521.941
plotCombMultSamples3.1200.0683.188
plotCombination2genes2.4720.0682.540
plotLogRatio3.7980.1283.926
probabilitiesPlot0.0010.0000.001
probe2gene1.4340.0441.478
profilesPlot1.6610.0441.705
propdegenescalculation2.2580.1002.357
replicates0.0020.0000.001
spectralMap9.5350.3169.851
tTest1.9860.0322.017
volcanoPlot2.1350.0282.163