Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1812/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RTCA 1.58.0 (landing page) Jitao David Zhang
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the RTCA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RTCA.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: RTCA |
Version: 1.58.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:RTCA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RTCA_1.58.0.tar.gz |
StartedAt: 2024-11-20 11:55:08 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 11:55:50 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 42.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: RTCA.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:RTCA.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RTCA_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RTCA.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RTCA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘RTCA’ version ‘1.58.0’ * checking package namespace information ... OK * checking package dependencies ... OK * 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 ‘RTCA’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ 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 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) RTCA-class.Rd:79: Lost braces 79 | \item{expID}{code{signature(object = "RTCA")}: get Experiment ID} | ^ checkRd: (-1) RTCA-class.Rd:80: Lost braces 80 | \item{expID<-}{code{signature(object = "RTCA", value = "ANY")}: set Experiment ID} | ^ * 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 ... WARNING Documented arguments not in \usage in Rd file 'interpolationTransform.Rd': ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘essentials.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/RTCA.Rcheck/00check.log’ for details.
RTCA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL RTCA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘RTCA’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** 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 (RTCA)
RTCA.Rcheck/tests/essentials.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(RTCA) Loading required package: Biobase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: RColorBrewer Loading required package: gtools > > > tl <- new("RTCAtimeline") > timeUnit(tl) <- "hour" > startTime(tl) <- Sys.time()-3e6 > show(tl) RTCAtimeline ================================================ time action 0 start ================================================ Time unit: hour RTCA-run start time: 2024-10-16 18:35:45.158059 > > tl2 <- addAction(tl, 1, "seeding") > show(tl2) RTCAtimeline ================================================ time action 0 start 1 seeding ================================================ Time unit: hour RTCA-run start time: 2024-10-16 18:35:45.158059 > stopifnot(getAction(tl2, 0)=="start") > stopifnot(is.null(getAction(tl2, -1))) > > rmAction(tl2, 0) RTCAtimeline ================================================ time action 1 seeding ================================================ Time unit: hour RTCA-run start time: 2024-10-16 18:35:45.158059 > rmAction(tl2, 1) RTCAtimeline ================================================ time action 0 start ================================================ Time unit: hour RTCA-run start time: 2024-10-16 18:35:45.158059 > rmAction(tl2, -1) RTCAtimeline ================================================ time action 0 start 1 seeding ================================================ Time unit: hour RTCA-run start time: 2024-10-16 18:35:45.158059 > > updateAction(tl2, 1, "not seeding") RTCAtimeline ================================================ time action 0 start 1 not seeding ================================================ Time unit: hour RTCA-run start time: 2024-10-16 18:35:45.158059 > updateAction(tl2, -1,"not seeding") RTCAtimeline ================================================ time action -1 not seeding 0 start 1 seeding ================================================ Time unit: hour RTCA-run start time: 2024-10-16 18:35:45.158059 > updateAction(tl2, -1,"not seeding", ifnotfound="ignore") RTCAtimeline ================================================ time action 0 start 1 seeding ================================================ Time unit: hour RTCA-run start time: 2024-10-16 18:35:45.158059 > startTime(tl2) <- as.POSIXct("2009-05-06 14:52:03") > tl2 RTCAtimeline ================================================ time action 0 start 1 seeding ================================================ Time unit: hour RTCA-run start time: 2009-05-06 14:52:03 > > ofile <- system.file("/extdata/testOutput.csv", package="RTCA") > x <- parseRTCA(ofile) Read 245 items > > ## add actions to timeline > x <- addAction(x, 22, "transfection") > x <- addAction(x, 30, "change medium") > > xr <- ratioTransform(x, 35) > xrs <- smoothTransform(xr) > xi <- interpolationTransform(x) > xd <- derivativeTransform(x) > xrgr <- rgrTransform(x) > #plotRTCA(xrgr, xlim=c(35, 80), ylim=c(-0.2, 0.2)) > plot(sliceRTCA(x,0, 80)[,c(11,13)], type="l", col="black", ylim=c(0, 1.5)) > abline(h=0, col=2, lty=5) > plot(sliceRTCA(xrgr, 20, 80)[,c(11,13)], type="l", col="black") > abline(h=0, col=2, lty=5) > > plotGridEffect(x) > plotGridEffect(x, "col") > plateView(sliceRTCA(x, 0, 80)) > > proc.time() user system elapsed 2.441 0.117 2.462
RTCA.Rcheck/RTCA-Ex.timings
name | user | system | elapsed | |
RTCA-class | 0.368 | 0.020 | 0.390 | |
RTCAtimeline-class | 0.002 | 0.000 | 0.002 | |
alphaNames | 0.003 | 0.000 | 0.003 | |
combineRTCA | 0.216 | 0.000 | 0.218 | |
controlView | 0.190 | 0.000 | 0.191 | |
derivativeTransform | 0.197 | 0.000 | 0.202 | |
factor2numeric | 0.001 | 0.000 | 0.001 | |
interpolationTransform | 0.264 | 0.040 | 0.304 | |
nearestTimeIndex | 0.189 | 0.015 | 0.204 | |
parseRTCA | 0.635 | 0.000 | 0.636 | |
plateView | 0.3 | 0.0 | 0.3 | |
plotGridEffect | 0.391 | 0.000 | 0.392 | |
ratioTransform | 0.151 | 0.004 | 0.155 | |
rgrTransform | 0.513 | 0.020 | 0.534 | |
sliceRTCA | 0.179 | 0.004 | 0.184 | |
smoothTransform | 0.312 | 0.000 | 0.313 | |
spectramaxImport | 0.006 | 0.004 | 0.013 | |