Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-23 12:08 -0400 (Sat, 23 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4821 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4599 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4553 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
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 2060/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spicyR 1.21.2 (landing page) Ellis Patrick
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / 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: 1.21.2 |
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_1.21.2.tar.gz |
StartedAt: 2025-08-22 12:43:44 -0000 (Fri, 22 Aug 2025) |
EndedAt: 2025-08-22 12:50:24 -0000 (Fri, 22 Aug 2025) |
EllapsedTime: 399.5 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_1.21.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/spicyR.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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 ‘spicyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spicyR’ version ‘1.21.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 28 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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’ .format_data: no visible binding for global variable ‘cellType’ bubblePlot: no visible binding for global variable ‘parent’ bubblePlot: no visible binding for global variable ‘cellTypeB_id’ bubblePlot: no visible binding for global variable ‘cellTypeB_numeric’ 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 ‘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’ 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’ inhomLPair: no visible binding for global variable ‘cellTypeI’ inhomLPair: no visible binding for global variable ‘cellTypeJ’ plotImage: no visible binding for global variable ‘x’ plotImage: no visible binding for global variable ‘y’ plotImage: no visible binding for global variable ‘density’ plotImage: no visible binding for global variable ‘cellTypeNew’ spatialSurv : <anonymous>: no visible global function definition for ‘pchisq’ spatialSurv: no visible binding for global variable ‘test’ spatialSurv: no visible binding for global variable ‘coef’ spatialSurv: no visible binding for global variable ‘se.coef’ spatialSurv: no visible binding for global variable ‘p.value’ spicy: no visible global function definition for ‘relevel’ spicyBoxPlot: no visible binding for global variable ‘condition’ spicyBoxPlot: no visible binding for global variable ‘pairwiseAssoc’ survBubble: no visible binding for global variable ‘test’ survBubble: no visible binding for global variable ‘parent’ survBubble: no visible binding for global variable ‘to’ survBubble: no visible binding for global variable ‘from’ survBubble: no visible binding for global variable ‘p.value’ survBubble: no visible binding for global variable ‘logP’ survBubble: no visible binding for global variable ‘coef’ survBubble: no visible binding for global variable ‘sig’ Undefined global functions or variables: . association cellID cellType cellTypeB_id cellTypeB_numeric cellTypeI cellTypeJ cellTypeNew cellType_from cellType_to coef condition d density from i imageCellID imageID j logP n_close one p.value pairwiseAssoc parent pchisq relevel rowname se.coef sig test to value wt x y Consider adding importFrom("stats", "coef", "density", "pchisq", "relevel") to your NAMESPACE file. * 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 23.335 0.343 23.742 convPairs 15.234 0.512 15.807 getPairwise 7.304 0.200 7.503 * 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] 0.900716577 - 0.900716396 [1] [2] 0.872831518 - 0.872831224 [2] [3] 0.985083470 - 0.985083010 [3] [4] 1.056566405 - 1.056565888 [4] [5] 0.885611269 - 0.885610907 [5] [6] 0.917185360 - 0.917185203 [6] [7] 1.291070495 - 1.291071205 [7] [8] 0.966434151 - 0.966433660 [8] [9] 0.910787063 - 0.910786914 [9] [10] 1.130604144 - 1.130603861 [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-3.22-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-4.5.0/site-library’ * installing *source* package ‘spicyR’ ... ** this is package ‘spicyR’ version ‘1.21.2’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 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") Dropping unused levels. Using stage = Non-diabetic as base comparison group. If this is not the desired base group, please convert cells$stage into a factor and change the order of levels(cells$stage) so that the base group is at index 1. [ FAIL 1 | WARN 0 | SKIP 0 | PASS 5 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-spicyR.R:7:9'): the output is equal to previous version ────── suppressWarnings(...) (`actual`) not equal to `original_result` (`expected`). actual@.Data[[1]] vs expected@.Data[[1]] (Intercept) conditionOnset conditionLong-duration - actual@.Data[[1]][1, ] 1.622665 5.961819 10.58897 + expected@.Data[[1]][1, ] 1.622667 5.961804 10.58897 `actual@.Data[[1]]$(Intercept)`: 1.6226650 `expected@.Data[[1]]$(Intercept)`: 1.6226675 `actual@.Data[[1]]$conditionOnset`: 5.961819 `expected@.Data[[1]]$conditionOnset`: 5.961804 `actual@.Data[[1]]$conditionLong-duration`: 10.58896862 `expected@.Data[[1]]$conditionLong-duration`: 10.58896896 actual@.Data[[3]] vs expected@.Data[[3]] (Intercept) conditionOnset conditionLong-duration - actual@.Data[[3]][1, ] 0.8528760 0.6122504 0.3825388 + expected@.Data[[3]][1, ] 0.8528758 0.6122512 0.3825387 `actual@.Data[[3]]$(Intercept)`: 0.85287599 `expected@.Data[[3]]$(Intercept)`: 0.85287576 `actual@.Data[[3]]$conditionOnset`: 0.61225038 `expected@.Data[[3]]$conditionOnset`: 0.61225121 `actual@.Data[[3]]$conditionLong-duration`: 0.382538768 `expected@.Data[[3]]$conditionLong-duration`: 0.382538702 `actual@.Data[[4]]$(Intercept)`: 8.73055236 `expected@.Data[[4]]$(Intercept)`: 8.73055175 `actual@.Data[[4]]$conditionOnset`: 11.7306002 `expected@.Data[[4]]$conditionOnset`: 11.7305984 `actual@.Data[[4]]$conditionLong-duration`: 12.0805714 `expected@.Data[[4]]$conditionLong-duration`: 12.0805702 actual@.Data[[5]] vs expected@.Data[[5]] (Intercept) conditionOnset conditionLong-duration - actual@.Data[[5]][1, ] 0.1858605 0.5082280 0.8765288 + expected@.Data[[5]][1, ] 0.1858608 0.5082268 0.8765289 `actual@.Data[[5]]$(Intercept)`: 0.18586052 `expected@.Data[[5]]$(Intercept)`: 0.18586082 `actual@.Data[[5]]$conditionOnset`: 0.5082280 `expected@.Data[[5]]$conditionOnset`: 0.5082268 `actual@.Data[[5]]$conditionLong-duration`: 0.87652879 `expected@.Data[[5]]$conditionLong-duration`: 0.87652891 actual@.Data[[8]]$Tc__Th | expected@.Data[[8]]$Tc__Th [67] 14.828620658 | 14.828620658 [67] [68] 7.864179684 | 7.864179684 [68] [69] 2.798068612 | 2.798068612 [69] [70] 10.447586876 - 10.447060880 [70] [71] 68.398894238 | 68.398894238 [71] [72] -170.000000000 | -170.000000000 [72] [73] 71.405466103 | 71.405466103 [73] actual@.Data[[10]]$Tc__Th | expected@.Data[[10]]$Tc__Th [1] 0.900716577 - 0.900716396 [1] [2] 0.872831518 - 0.872831224 [2] [3] 0.985083470 - 0.985083010 [3] [4] 1.056566405 - 1.056565888 [4] [5] 0.885611269 - 0.885610907 [5] [6] 0.917185360 - 0.917185203 [6] [7] 1.291070495 - 1.291071205 [7] [8] 0.966434151 - 0.966433660 [8] [9] 0.910787063 - 0.910786914 [9] [10] 1.130604144 - 1.130603861 [10] ... ... ... and 110 more ... actual$coefficient vs expected$coefficient (Intercept) conditionOnset conditionLong-duration - actual$coefficient[1, ] 1.622665 5.961819 10.58897 + expected$coefficient[1, ] 1.622667 5.961804 10.58897 `actual$coefficient$(Intercept)`: 1.6226650 `expected$coefficient$(Intercept)`: 1.6226675 `actual$coefficient$conditionOnset`: 5.961819 `expected$coefficient$conditionOnset`: 5.961804 `actual$coefficient$conditionLong-duration`: 10.58896862 `expected$coefficient$conditionLong-duration`: 10.58896896 actual$p.value vs expected$p.value (Intercept) conditionOnset conditionLong-duration - actual$p.value[1, ] 0.8528760 0.6122504 0.3825388 + expected$p.value[1, ] 0.8528758 0.6122512 0.3825387 `actual$p.value$(Intercept)`: 0.85287599 `expected$p.value$(Intercept)`: 0.85287576 `actual$p.value$conditionOnset`: 0.61225038 `expected$p.value$conditionOnset`: 0.61225121 `actual$p.value$conditionLong-duration`: 0.382538768 `expected$p.value$conditionLong-duration`: 0.382538702 `actual$se$(Intercept)`: 8.73055236 `expected$se$(Intercept)`: 8.73055175 `actual$se$conditionOnset`: 11.7306002 `expected$se$conditionOnset`: 11.7305984 `actual$se$conditionLong-duration`: 12.0805714 `expected$se$conditionLong-duration`: 12.0805702 actual$statistic vs expected$statistic (Intercept) conditionOnset conditionLong-duration - actual$statistic[1, ] 0.1858605 0.5082280 0.8765288 + expected$statistic[1, ] 0.1858608 0.5082268 0.8765289 `actual$statistic$(Intercept)`: 0.18586052 `expected$statistic$(Intercept)`: 0.18586082 `actual$statistic$conditionOnset`: 0.5082280 `expected$statistic$conditionOnset`: 0.5082268 `actual$statistic$conditionLong-duration`: 0.87652879 `expected$statistic$conditionLong-duration`: 0.87652891 actual$pairwiseAssoc$Tc__Th | expected$pairwiseAssoc$Tc__Th [67] 14.828620658 | 14.828620658 [67] [68] 7.864179684 | 7.864179684 [68] [69] 2.798068612 | 2.798068612 [69] [70] 10.447586876 - 10.447060880 [70] [71] 68.398894238 | 68.398894238 [71] [72] -170.000000000 | -170.000000000 [72] [73] 71.405466103 | 71.405466103 [73] actual$weights$Tc__Th | expected$weights$Tc__Th [1] 0.900716577 - 0.900716396 [1] [2] 0.872831518 - 0.872831224 [2] [3] 0.985083470 - 0.985083010 [3] [4] 1.056566405 - 1.056565888 [4] [5] 0.885611269 - 0.885610907 [5] [6] 0.917185360 - 0.917185203 [6] [7] 1.291070495 - 1.291071205 [7] [8] 0.966434151 - 0.966433660 [8] [9] 0.910787063 - 0.910786914 [9] [10] 1.130604144 - 1.130603861 [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 | 0.023 | 0.004 | 0.028 | |
colTest | 1.324 | 0.124 | 1.451 | |
convPairs | 15.234 | 0.512 | 15.807 | |
getPairwise | 7.304 | 0.200 | 7.503 | |
getProp | 0.323 | 0.012 | 0.336 | |
plotImage | 1.066 | 0.004 | 1.073 | |
signifPlot | 1.588 | 0.067 | 1.666 | |
spicy | 23.335 | 0.343 | 23.742 | |
spicyBoxPlot | 0.387 | 0.000 | 0.388 | |
topPairs | 0.011 | 0.004 | 0.014 | |