Back to Multiple platform build/check report for BioC 3.21: simplified long |
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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 708/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
findIPs 1.3.1 (landing page) Shuo Wang
| 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 findIPs package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/findIPs.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: findIPs |
Version: 1.3.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:findIPs.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings findIPs_1.3.1.tar.gz |
StartedAt: 2024-12-24 06:44:39 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 06:54:04 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 564.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: findIPs.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:findIPs.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings findIPs_1.3.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/findIPs.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 ‘findIPs/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘findIPs’ version ‘1.3.1’ * package encoding: UTF-8 * 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 ‘findIPs’ 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 ...Warning: program compiled against libxml 212 using older 211 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 ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed findIPs 45.094 0.230 45.423 sumRanks 35.084 0.028 35.199 plotRankScatters 35.029 0.027 35.121 getdrop1ranks 34.739 0.018 34.828 plotIPs 34.267 0.016 34.354 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: OK
findIPs.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL findIPs ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘findIPs’ ... ** using staged installation ** R ** data ** 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 (findIPs)
findIPs.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 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(testthat) > library(findIPs) > > # get data > data(miller05) > X <- miller05$X > y <- miller05$y > surv <- miller05$surv > > # save expected results > > # obj <- getdrop1ranks(X, y, > # fun = "t.test", > # decreasing = FALSE, > # topN = 100) > # > # expected.t.adaptive <- sumRanks(origRank = obj$origRank, > # drop1Rank = obj$drop1Rank, > # topN = 100, > # method = "adaptive") > # > # expected.t.unweighted <- sumRanks(origRank = obj$origRank, > # drop1Rank = obj$drop1Rank, > # topN = 100, > # method = "unweighted") > # > # expected.t.weighted <- sumRanks(origRank = obj$origRank, > # drop1Rank = obj$drop1Rank, > # topN = 100, > # method = "weightedSpearman") > # > # expected.t.adaptive.ipsr <- findIPs(X, y, > # fun = "t.test", > # decreasing = FALSE, > # topN = 100, > # method = "adaptive") > # > # expected.cox.adaptive.ipsr <- findIPs(X, surv, > # fun = "cox", > # decreasing = FALSE, > # topN = 100, > # method = "adaptive") > # > # save(list = c("expected.t.adaptive", "expected.t.unweighted", > # "expected.t.weighted", "expected.t.adaptive.ipsr", > # "expected.cox.adaptive.ipsr"), > # file = "./expectedResults/expectedResults.RData") > > # get observed results > > load("./expectedResults/expectedResults.RData") > > obj <- getdrop1ranks(X, y, + fun = "t.test", + decreasing = FALSE, + topN = 100) > > observed.t.adaptive <- sumRanks(origRank = obj$origRank, + drop1Rank = obj$drop1Rank, + topN = 100, + method = "adaptive") > > observed.t.unweighted <- sumRanks(origRank = obj$origRank, + drop1Rank = obj$drop1Rank, + topN = 100, + method = "unweighted") > > observed.t.weighted <- sumRanks(origRank = obj$origRank, + drop1Rank = obj$drop1Rank, + topN = 100, + method = "weightedSpearman") > > observed.t.adaptive.ipsr <- findIPs(X, y, + fun = "t.test", + decreasing = FALSE, + topN = 100, + method = "adaptive") > > observed.cox.adaptive.ipsr <- findIPs(X, surv, + fun = "cox", + decreasing = FALSE, + topN = 100, + method = "adaptive") > > test_that("test getdrop1ranks and sumRanks",{ + expect_equal(expected.t.adaptive, observed.t.adaptive) + expect_equal(expected.t.unweighted, observed.t.unweighted) + expect_equal(expected.t.weighted, expected.t.weighted) + }) Test passed 🎉 > > test_that("stepwise(getdrop1ranks and sumRanks) and one-step procedure",{ + expect_equal(observed.t.adaptive.ipsr, observed.t.adaptive) + }) Test passed 🎊 > > test_that("test ipsr",{ + expect_equal(expected.t.adaptive.ipsr, observed.t.adaptive.ipsr) + }) Test passed 😀 > > test_that("test ipsr for survival outcomes (ranked by univariate cox)",{ + expect_equal(expected.cox.adaptive.ipsr, observed.cox.adaptive.ipsr) + }) Test passed 🥳 > > > > > > proc.time() user system elapsed 200.824 2.559 203.830
findIPs.Rcheck/findIPs-Ex.timings
name | user | system | elapsed | |
findIPs | 45.094 | 0.230 | 45.423 | |
getdrop1ranks | 34.739 | 0.018 | 34.828 | |
miller05 | 0.011 | 0.004 | 0.015 | |
plotAdaptiveWeights | 0.009 | 0.000 | 0.009 | |
plotIPs | 34.267 | 0.016 | 34.354 | |
plotRankScatters | 35.029 | 0.027 | 35.121 | |
sumRanks | 35.084 | 0.028 | 35.199 | |