Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:02:48 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 2/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
a4Base 1.52.0 (landing page) Laure Cougnaud
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
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. |
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: 2024-05-31 01:05:17 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 01:08:22 -0400 (Fri, 31 May 2024) |
EllapsedTime: 184.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: a4Base.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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 9.146 0.339 9.487 * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/a4Base.Rcheck/00check.log’ for details.
a4Base.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
a4Base.Rcheck/a4Base-Ex.timings
name | user | system | elapsed | |
a4palette | 0.044 | 0.000 | 0.044 | |
addQuantilesColors | 1.748 | 0.172 | 1.920 | |
boxPlot | 2.449 | 0.108 | 2.556 | |
combineTwoExpressionSet | 0.001 | 0.000 | 0.000 | |
computeLogRatio | 4.157 | 0.184 | 4.341 | |
createExpressionSet | 0.030 | 0.000 | 0.031 | |
filterVarInt | 2.178 | 0.072 | 2.250 | |
heatmap.expressionSet | 0.002 | 0.000 | 0.002 | |
histPvalue | 1.739 | 0.044 | 1.783 | |
histpvalueplotter | 1.683 | 0.039 | 1.723 | |
lassoReg | 1.693 | 0.056 | 1.749 | |
logReg | 0.000 | 0.000 | 0.001 | |
nlcvTT | 0 | 0 | 0 | |
plot1gene | 1.675 | 0.055 | 1.730 | |
plotComb2Samples | 1.854 | 0.068 | 1.923 | |
plotCombMultSamples | 3.023 | 0.100 | 3.123 | |
plotCombination2genes | 2.454 | 0.048 | 2.502 | |
plotLogRatio | 3.722 | 0.080 | 3.802 | |
probabilitiesPlot | 0.001 | 0.000 | 0.001 | |
probe2gene | 1.390 | 0.084 | 1.474 | |
profilesPlot | 1.654 | 0.058 | 1.712 | |
propdegenescalculation | 2.119 | 0.088 | 2.207 | |
replicates | 0.002 | 0.000 | 0.002 | |
spectralMap | 9.146 | 0.339 | 9.487 | |
tTest | 1.956 | 0.039 | 1.996 | |
volcanoPlot | 2.117 | 0.031 | 2.149 | |