Laure Cougnaud
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 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) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:29 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the a4Base package: - 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: /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_1.52.0.tar.gz |
| StartedAt: 2024-05-06 19:29:47 -0400 (Mon, 06 May 2024) |
| EndedAt: 2024-05-06 19:31:03 -0400 (Mon, 06 May 2024) |
| EllapsedTime: 75.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: a4Base.Rcheck |
| Warnings: 0 |
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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_1.52.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/a4Base.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* 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 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 ... 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
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/a4Base.Rcheck/00check.log’
for details.
a4Base.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL a4Base ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 | 0.013 | 0.000 | 0.014 | |
| addQuantilesColors | 0.975 | 0.049 | 1.038 | |
| boxPlot | 1.098 | 0.020 | 1.121 | |
| combineTwoExpressionSet | 0 | 0 | 0 | |
| computeLogRatio | 1.703 | 0.043 | 1.747 | |
| createExpressionSet | 0.009 | 0.000 | 0.009 | |
| filterVarInt | 0.968 | 0.035 | 1.004 | |
| heatmap.expressionSet | 0.001 | 0.000 | 0.001 | |
| histPvalue | 0.824 | 0.016 | 0.840 | |
| histpvalueplotter | 0.821 | 0.016 | 0.838 | |
| lassoReg | 0.830 | 0.014 | 0.844 | |
| logReg | 0 | 0 | 0 | |
| nlcvTT | 0 | 0 | 0 | |
| plot1gene | 0.808 | 0.014 | 0.823 | |
| plotComb2Samples | 0.860 | 0.019 | 0.882 | |
| plotCombMultSamples | 1.340 | 0.038 | 1.379 | |
| plotCombination2genes | 1.287 | 0.015 | 1.303 | |
| plotLogRatio | 1.552 | 0.065 | 1.619 | |
| probabilitiesPlot | 0 | 0 | 0 | |
| probe2gene | 0.698 | 0.007 | 0.705 | |
| profilesPlot | 0.789 | 0.012 | 0.801 | |
| propdegenescalculation | 1.030 | 0.024 | 1.054 | |
| replicates | 0.000 | 0.000 | 0.001 | |
| spectralMap | 4.047 | 0.147 | 4.195 | |
| tTest | 0.916 | 0.020 | 0.937 | |
| volcanoPlot | 0.995 | 0.021 | 1.017 | |