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 |
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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 1633/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
qsmooth 1.22.0 (landing page) Stephanie C. Hicks
| 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 qsmooth package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/qsmooth.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: qsmooth |
Version: 1.22.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:qsmooth.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings qsmooth_1.22.0.tar.gz |
StartedAt: 2024-11-20 11:19:26 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 11:24:13 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 286.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: qsmooth.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:qsmooth.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings qsmooth_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/qsmooth.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 ‘qsmooth/DESCRIPTION’ ... OK * this is package ‘qsmooth’ version ‘1.22.0’ * 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 ‘qsmooth’ 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 ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented data sets: ‘gc’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 * 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: 1 WARNING See ‘/home/biocbuild/bbs-3.20-bioc/meat/qsmooth.Rcheck/00check.log’ for details.
qsmooth.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL qsmooth ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘qsmooth’ ... ** 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 (qsmooth)
qsmooth.Rcheck/tests/testthat.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(testthat) > context("checking the qsmooth function") > > library(qsmooth) > > test_that("checking dimensions of qsmooth object", { + n_genes <- 1000 + n_samples <- 10 + set.seed(1234) + x <- matrix(rnorm(n_genes*n_samples), n_genes, n_samples) + group_factor <- rep(c(1,2),each=5) + qs_norm <- qsmooth(object = x, + group_factor = group_factor) + + expect_equal(length(qsmoothWeights(qs_norm)), n_genes) + expect_equal(nrow(qsmoothData(qs_norm)), n_genes) + expect_equal(ncol(qsmoothData(qs_norm)), n_samples) + }) Test passed 🥇 > > test_that("checking qsmooth normalized data", { + n_genes <- 1000 + n_samples <- 10 + set.seed(1234) + x <- matrix(rnorm(n_genes*n_samples), n_genes, n_samples) + group_factor <- rep(c(1,2),each=5) + qs_norm <- qsmooth(object = x, group_factor = group_factor) + expect_equal(qsmoothData(qs_norm)[1,1], -1.25856, tolerance = .0001) + expect_equal(qsmoothWeights(qs_norm)[1], 0.97495, tolerance = .0001) + }) Test passed 🥇 > > > test_that("checking qsmoothGC normalized data", { + n_genes <- 1000 + n_samples <- 10 + set.seed(1234) + x <- matrix(rpois(n_genes*n_samples, lambda=12), n_genes, n_samples) + group_factor <- rep(c(1,2),each=5) + gc <- runif(n=n_genes, min=0.2, max=0.9) + ## one group should be same as qsmooth + qs_norm <- qsmooth(object = x, group_factor = group_factor) + qs_normGC <- qsmoothGC(object = x, + gc = gc, + group_factor = group_factor, + nGroups = 1, + round = FALSE) + expect_equal(qsmoothData(qs_norm), qsmoothData(qs_normGC), tolerance = .001) + }) Test passed 🥇 > > proc.time() user system elapsed 14.474 0.962 15.437
qsmooth.Rcheck/qsmooth-Ex.timings
name | user | system | elapsed | |
qsmooth-class | 0.010 | 0.000 | 0.009 | |
qsmooth | 0.005 | 0.000 | 0.005 | |
qsmoothData | 0.01 | 0.00 | 0.01 | |
qsmoothGC | 0.187 | 0.000 | 0.188 | |
qsmoothPlotWeights | 0.007 | 0.000 | 0.008 | |
qsmoothWeights | 0.005 | 0.000 | 0.005 | |
qstats | 0.003 | 0.000 | 0.003 | |