Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-02-21 12:52:59 -0500 (Wed, 21 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4657
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4397
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 2/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
a4Base 1.51.0  (landing page)
Laure Cougnaud
Snapshot Date: 2024-02-20 14:10:09 -0500 (Tue, 20 Feb 2024)
git_url: https://git.bioconductor.org/packages/a4Base
git_branch: devel
git_last_commit: 84de708
git_last_commit_date: 2023-10-24 09:46:28 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published

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: 1.51.0
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_1.51.0.tar.gz
StartedAt: 2024-02-20 20:00:05 -0500 (Tue, 20 Feb 2024)
EndedAt: 2024-02-20 20:03:19 -0500 (Tue, 20 Feb 2024)
EllapsedTime: 194.4 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_1.51.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/a4Base.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.51.0’
* 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 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) 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 9.396  0.203   9.602
* 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
###
##############################################################################
##############################################################################


* 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
a4palette0.0400.0030.044
addQuantilesColors1.9350.1522.086
boxPlot2.4010.1842.585
combineTwoExpressionSet000
computeLogRatio4.3240.1444.467
createExpressionSet0.0300.0000.031
filterVarInt2.1450.0362.181
heatmap.expressionSet0.0000.0020.002
histPvalue1.7620.0411.803
histpvalueplotter1.7430.0291.772
lassoReg1.8430.0431.886
logReg000
nlcvTT0.0000.0010.000
plot1gene1.7590.0271.786
plotComb2Samples1.8930.0601.954
plotCombMultSamples2.5830.0752.659
plotCombination2genes2.4660.0512.518
plotLogRatio4.5180.1454.662
probabilitiesPlot000
probe2gene1.4850.0401.525
profilesPlot1.6750.0351.711
propdegenescalculation1.7280.0401.768
replicates0.0010.0000.001
spectralMap9.3960.2039.602
tTest1.9600.0392.000
volcanoPlot2.1300.0362.166