Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-02 11:45 -0400 (Tue, 02 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4693 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4413 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4356 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4407 |
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 1993/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spicyR 1.17.1 (landing page) Ellis Patrick
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the spicyR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/spicyR.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: spicyR |
Version: 1.17.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:spicyR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings spicyR_1.17.1.tar.gz |
StartedAt: 2024-07-02 09:50:21 -0000 (Tue, 02 Jul 2024) |
EndedAt: 2024-07-02 09:56:44 -0000 (Tue, 02 Jul 2024) |
EllapsedTime: 382.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: spicyR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:spicyR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings spicyR_1.17.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/spicyR.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘spicyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spicyR’ version ‘1.17.1’ * 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 ‘spicyR’ 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 ... NOTE .format_data: no visible binding for global variable ‘imageID’ bubblePlot: no visible binding for global variable ‘condition’ convPairs: no visible binding for global variable ‘rowname’ convPairs: no visible binding for global variable ‘cellType_from’ convPairs: no visible binding for global variable ‘cellType_to’ convPairs: no visible binding for global variable ‘one’ convPairs: no visible binding for global variable ‘n_close’ convPairs: no visible binding for global variable ‘n’ convPairs: no visible binding for global variable ‘test’ convPairs: no visible binding for global variable ‘association’ getCellSummary: no visible binding for global variable ‘cellID’ getCellSummary: no visible binding for global variable ‘imageCellID’ getCellSummary: no visible binding for global variable ‘x’ getCellSummary: no visible binding for global variable ‘y’ getCellSummary: no visible binding for global variable ‘cellType’ getCellSummary: no visible binding for global variable ‘.’ getCellType: no visible binding for global variable ‘cellType’ getImagePheno: no visible binding for global variable ‘cellID’ getImagePheno: no visible binding for global variable ‘imageCellID’ getImagePheno: no visible binding for global variable ‘y’ getImagePheno: no visible binding for global variable ‘cellType’ getImagePheno: no visible binding for global variable ‘.’ inhomL: no visible binding for global variable ‘j’ inhomL: no visible binding for global variable ‘value’ inhomL: no visible binding for global variable ‘i’ inhomL: no visible binding for global variable ‘d’ inhomL: no visible binding for global variable ‘cellTypeI’ inhomL: no visible binding for global variable ‘cellTypeJ’ inhomL: no visible global function definition for ‘.’ inhomL: no visible binding for global variable ‘wt’ spicyBoxPlot: no visible binding for global variable ‘condition’ spicyBoxPlot: no visible binding for global variable ‘imageID’ Undefined global functions or variables: . association cellID cellType cellTypeI cellTypeJ cellType_from cellType_to condition d i imageCellID imageID j n n_close one rowname test value wt x y * 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 LazyData ... 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 spicy 18.554 0.096 18.669 convPairs 16.330 0.487 16.856 getPairwise 8.820 0.172 8.956 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: [1] 0.93325927 - 0.93325919 [1] [2] 0.92472363 - 0.92472353 [2] [3] 1.00199084 | 1.00199084 [3] [4] 1.02269950 - 1.02269953 [4] [5] 0.96035490 - 0.96035484 [5] [6] 0.88132886 - 0.88132873 [6] [7] 1.09670638 - 1.09670650 [7] [8] 0.99659428 - 0.99659427 [8] [9] 0.87976285 - 0.87976272 [9] [10] 1.03910618 - 1.03910622 [10] ... ... ... and 110 more ... [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ] Error: Test failures Execution halted * 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 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/spicyR.Rcheck/00check.log’ for details.
spicyR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL spicyR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.0/site-library’ * installing *source* package ‘spicyR’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (spicyR)
spicyR.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 (2024-04-24) -- "Puppy Cup" 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(spicyR) > > test_check("spicyR") [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-spicyR.R:5:9'): the output is equal using segmented cells and SingleCellExperiment ── suppressWarnings(...) (`actual`) not equal to `original_result` (`expected`). actual@.Data[[1]] vs expected@.Data[[1]] (Intercept) conditionOnset conditionLong-duration - actual@.Data[[1]][1, ] 11.76378 9.266305 7.718953 + expected@.Data[[1]][1, ] 11.76378 9.266281 7.718956 `actual@.Data[[1]]$(Intercept)`: 11.763777 `expected@.Data[[1]]$(Intercept)`: 11.763781 `actual@.Data[[1]]$conditionOnset`: 9.26631 `expected@.Data[[1]]$conditionOnset`: 9.26628 `actual@.Data[[1]]$conditionLong-duration`: 7.718953 `expected@.Data[[1]]$conditionLong-duration`: 7.718956 actual@.Data[[3]] vs expected@.Data[[3]] (Intercept) conditionOnset conditionLong-duration - actual@.Data[[3]][1, ] 0.3861757 0.6171978 0.6823976 + expected@.Data[[3]][1, ] 0.3861755 0.6171987 0.6823975 `actual@.Data[[3]]$(Intercept)`: 0.3861757 `expected@.Data[[3]]$(Intercept)`: 0.3861755 `actual@.Data[[3]]$conditionOnset`: 0.6171978 `expected@.Data[[3]]$conditionOnset`: 0.6171987 `actual@.Data[[3]]$conditionLong-duration`: 0.6823976 `expected@.Data[[3]]$conditionLong-duration`: 0.6823975 `actual@.Data[[4]]$conditionOnset`: 18.4895927 `expected@.Data[[4]]$conditionOnset`: 18.4895919 `actual@.Data[[4]]$conditionLong-duration`: 18.8167976 `expected@.Data[[4]]$conditionLong-duration`: 18.8167972 actual@.Data[[5]] vs expected@.Data[[5]] (Intercept) conditionOnset conditionLong-duration - actual@.Data[[5]][1, ] 0.8698276 0.5011633 0.4102161 + expected@.Data[[5]][1, ] 0.8698278 0.5011620 0.4102162 `actual@.Data[[5]]$(Intercept)`: 0.8698276 `expected@.Data[[5]]$(Intercept)`: 0.8698278 `actual@.Data[[5]]$conditionOnset`: 0.501163 `expected@.Data[[5]]$conditionOnset`: 0.501162 `actual@.Data[[5]]$conditionLong-duration`: 0.4102161 `expected@.Data[[5]]$conditionLong-duration`: 0.4102162 actual@.Data[[8]]$Tc__Th | expected@.Data[[8]]$Tc__Th [67] 37.43187272 | 37.43187272 [67] [68] 22.47521416 | 22.47521416 [68] [69] 5.97064882 | 5.97064882 [69] [70] 30.07529428 - 30.07429712 [70] [71] -60.25225482 | -60.25225482 [71] [72] -170.00000000 | -170.00000000 [72] [73] 212.40335640 | 212.40335640 [73] actual@.Data[[10]]$Tc__Th | expected@.Data[[10]]$Tc__Th [1] 0.93325927 - 0.93325919 [1] [2] 0.92472363 - 0.92472353 [2] [3] 1.00199084 | 1.00199084 [3] [4] 1.02269950 - 1.02269953 [4] [5] 0.96035490 - 0.96035484 [5] [6] 0.88132886 - 0.88132873 [6] [7] 1.09670638 - 1.09670650 [7] [8] 0.99659428 - 0.99659427 [8] [9] 0.87976285 - 0.87976272 [9] [10] 1.03910618 - 1.03910622 [10] ... ... ... and 110 more ... actual$coefficient vs expected$coefficient (Intercept) conditionOnset conditionLong-duration - actual$coefficient[1, ] 11.76378 9.266305 7.718953 + expected$coefficient[1, ] 11.76378 9.266281 7.718956 `actual$coefficient$(Intercept)`: 11.763777 `expected$coefficient$(Intercept)`: 11.763781 `actual$coefficient$conditionOnset`: 9.26631 `expected$coefficient$conditionOnset`: 9.26628 `actual$coefficient$conditionLong-duration`: 7.718953 `expected$coefficient$conditionLong-duration`: 7.718956 actual$p.value vs expected$p.value (Intercept) conditionOnset conditionLong-duration - actual$p.value[1, ] 0.3861757 0.6171978 0.6823976 + expected$p.value[1, ] 0.3861755 0.6171987 0.6823975 `actual$p.value$(Intercept)`: 0.3861757 `expected$p.value$(Intercept)`: 0.3861755 `actual$p.value$conditionOnset`: 0.6171978 `expected$p.value$conditionOnset`: 0.6171987 `actual$p.value$conditionLong-duration`: 0.6823976 `expected$p.value$conditionLong-duration`: 0.6823975 `actual$se$conditionOnset`: 18.4895927 `expected$se$conditionOnset`: 18.4895919 `actual$se$conditionLong-duration`: 18.8167976 `expected$se$conditionLong-duration`: 18.8167972 actual$statistic vs expected$statistic (Intercept) conditionOnset conditionLong-duration - actual$statistic[1, ] 0.8698276 0.5011633 0.4102161 + expected$statistic[1, ] 0.8698278 0.5011620 0.4102162 `actual$statistic$(Intercept)`: 0.8698276 `expected$statistic$(Intercept)`: 0.8698278 `actual$statistic$conditionOnset`: 0.501163 `expected$statistic$conditionOnset`: 0.501162 `actual$statistic$conditionLong-duration`: 0.4102161 `expected$statistic$conditionLong-duration`: 0.4102162 actual$pairwiseAssoc$Tc__Th | expected$pairwiseAssoc$Tc__Th [67] 37.43187272 | 37.43187272 [67] [68] 22.47521416 | 22.47521416 [68] [69] 5.97064882 | 5.97064882 [69] [70] 30.07529428 - 30.07429712 [70] [71] -60.25225482 | -60.25225482 [71] [72] -170.00000000 | -170.00000000 [72] [73] 212.40335640 | 212.40335640 [73] actual$weights$Tc__Th | expected$weights$Tc__Th [1] 0.93325927 - 0.93325919 [1] [2] 0.92472363 - 0.92472353 [2] [3] 1.00199084 | 1.00199084 [3] [4] 1.02269950 - 1.02269953 [4] [5] 0.96035490 - 0.96035484 [5] [6] 0.88132886 - 0.88132873 [6] [7] 1.09670638 - 1.09670650 [7] [8] 0.99659428 - 0.99659427 [8] [9] 0.87976285 - 0.87976272 [9] [10] 1.03910618 - 1.03910622 [10] ... ... ... and 110 more ... [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ] Error: Test failures Execution halted
spicyR.Rcheck/spicyR-Ex.timings
name | user | system | elapsed | |
bind | 0.025 | 0.000 | 0.025 | |
colTest | 2.924 | 0.048 | 2.977 | |
convPairs | 16.330 | 0.487 | 16.856 | |
getPairwise | 8.820 | 0.172 | 8.956 | |
getProp | 0.403 | 0.024 | 0.428 | |
signifPlot | 2.000 | 0.039 | 2.031 | |
spicy | 18.554 | 0.096 | 18.669 | |
spicyBoxPlot | 0.493 | 0.000 | 0.494 | |
topPairs | 0.019 | 0.000 | 0.019 | |