Laure Cougnaud
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/a4Base |
| git_branch: devel |
| git_last_commit: d78b7ff |
| git_last_commit_date: 2024-10-29 09:36:39 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 2/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| a4Base 1.55.0 (landing page) Laure Cougnaud
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: a4Base |
| Version: 1.55.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:a4Base.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings a4Base_1.55.0.tar.gz |
| StartedAt: 2024-12-24 03:34:47 -0000 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 03:38:52 -0000 (Tue, 24 Dec 2024) |
| EllapsedTime: 244.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: a4Base.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:a4Base.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings a4Base_1.55.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/a4Base.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.55.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
ExpressionSetWithComputation-class.Rd: ExpressionSet-class,
eSet-class, VersionedBiobase-class, Versioned-class
combineTwoExpressionSet.Rd: ExpressionSet-class
createExpressionSet.Rd: ExpressionSet-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 12.673 0.092 12.834
computeLogRatio 6.467 0.204 6.694
plotLogRatio 6.315 0.136 6.469
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/a4Base.Rcheck/00check.log’
for details.
a4Base.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL a4Base ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 | 0.043 | 0.016 | 0.059 | |
| addQuantilesColors | 1.908 | 0.071 | 1.996 | |
| boxPlot | 2.724 | 0.099 | 2.898 | |
| combineTwoExpressionSet | 0 | 0 | 0 | |
| computeLogRatio | 6.467 | 0.204 | 6.694 | |
| createExpressionSet | 0.044 | 0.000 | 0.044 | |
| filterVarInt | 2.524 | 0.052 | 2.586 | |
| heatmap.expressionSet | 0.000 | 0.000 | 0.001 | |
| histPvalue | 1.832 | 0.060 | 1.897 | |
| histpvalueplotter | 1.854 | 0.020 | 1.877 | |
| lassoReg | 1.784 | 0.056 | 1.843 | |
| logReg | 0 | 0 | 0 | |
| nlcvTT | 0.001 | 0.000 | 0.000 | |
| plot1gene | 1.735 | 0.032 | 1.771 | |
| plotComb2Samples | 1.864 | 0.035 | 1.907 | |
| plotCombMultSamples | 2.605 | 0.024 | 2.635 | |
| plotCombination2genes | 2.646 | 0.028 | 2.679 | |
| plotLogRatio | 6.315 | 0.136 | 6.469 | |
| probabilitiesPlot | 0 | 0 | 0 | |
| probe2gene | 1.465 | 0.032 | 1.502 | |
| profilesPlot | 1.701 | 0.032 | 1.736 | |
| propdegenescalculation | 1.882 | 0.024 | 1.913 | |
| replicates | 0.001 | 0.000 | 0.002 | |
| spectralMap | 12.673 | 0.092 | 12.834 | |
| tTest | 2.129 | 0.016 | 2.150 | |
| volcanoPlot | 2.300 | 0.028 | 2.563 | |