Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-19 11:47 -0400 (Wed, 19 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4742 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
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 2049/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spicyR 1.19.4 (landing page) Ellis Patrick
| 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 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
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. |
Package: spicyR |
Version: 1.19.4 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spicyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spicyR_1.19.4.tar.gz |
StartedAt: 2025-03-18 21:43:53 -0400 (Tue, 18 Mar 2025) |
EndedAt: 2025-03-18 21:45:56 -0400 (Tue, 18 Mar 2025) |
EllapsedTime: 123.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: spicyR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spicyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spicyR_1.19.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/spicyR.Rcheck’ * using R Under development (unstable) (2025-03-02 r87868) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘spicyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘spicyR’ version ‘1.19.4’ * 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 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’ spicyBoxPlot: no visible binding for global variable ‘condition’ 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 parent pchisq rowname se.coef sig test to value wt x y Consider adding importFrom("stats", "coef", "density", "pchisq") 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 8.777 0.524 4.982 * 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 NOTE See ‘/Users/biocbuild/bbs-3.21-bioc/meat/spicyR.Rcheck/00check.log’ for details.
spicyR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spicyR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘spicyR’ ... ** this is package ‘spicyR’ version ‘1.19.4’ ** 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
R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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") Skipping argument checks as `getPairwise()` is being called within `spicy()` [ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ] > > proc.time() user system elapsed 24.348 1.275 16.666
spicyR.Rcheck/spicyR-Ex.timings
name | user | system | elapsed | |
bind | 0.008 | 0.001 | 0.009 | |
colTest | 0.586 | 0.013 | 0.600 | |
convPairs | 4.413 | 0.196 | 4.636 | |
getPairwise | 2.776 | 0.141 | 2.491 | |
getProp | 0.209 | 0.015 | 0.118 | |
plotImage | 0.368 | 0.021 | 0.322 | |
signifPlot | 0.936 | 0.033 | 0.963 | |
spicy | 8.777 | 0.524 | 4.982 | |
spicyBoxPlot | 0.094 | 0.001 | 0.094 | |
topPairs | 0.044 | 0.021 | 0.069 | |