Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-22 11:35:22 -0400 (Wed, 22 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 3444
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: 2024-05-21 14:00:15 -0400 (Tue, 21 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
palomino3Windows Server 2022 Datacenter / x64  OK    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 palomino3


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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:a4Base.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings a4Base_1.52.0.tar.gz
StartedAt: 2024-05-21 22:52:12 -0400 (Tue, 21 May 2024)
EndedAt: 2024-05-21 22:55:46 -0400 (Tue, 21 May 2024)
EllapsedTime: 214.2 seconds
RetCode: 0
Status:   OK  
CheckDir: a4Base.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:a4Base.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings a4Base_1.52.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/a4Base.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'a4Base/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Base' version '1.52.0'
* 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 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 ... 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 10.98   1.21   12.19
* checking PDF version of manual ... OK
* DONE

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


Installation output

a4Base.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL a4Base
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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
a4palette0.030.000.03
addQuantilesColors2.000.212.61
boxPlot2.500.042.55
combineTwoExpressionSet000
computeLogRatio4.510.394.92
createExpressionSet0.050.000.05
filterVarInt2.140.222.36
heatmap.expressionSet000
histPvalue1.790.141.94
histpvalueplotter1.740.161.89
lassoReg1.750.121.87
logReg000
nlcvTT000
plot1gene1.880.132.00
plotComb2Samples1.780.091.88
plotCombMultSamples2.780.102.87
plotCombination2genes2.580.092.67
plotLogRatio4.480.194.68
probabilitiesPlot000
probe2gene1.360.061.42
profilesPlot1.570.061.63
propdegenescalculation2.120.092.22
replicates000
spectralMap10.98 1.2112.19
tTest2.210.252.47
volcanoPlot2.340.152.50