Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-02 12:11 -0400 (Sat, 02 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4535 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
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 2038/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
spatialFDA 1.1.3 (landing page) Martin Emons
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | 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 | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the spatialFDA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/spatialFDA.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: spatialFDA |
Version: 1.1.3 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spatialFDA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spatialFDA_1.1.3.tar.gz |
StartedAt: 2025-08-01 21:52:33 -0400 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 21:57:55 -0400 (Fri, 01 Aug 2025) |
EllapsedTime: 321.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: spatialFDA.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:spatialFDA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings spatialFDA_1.1.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/spatialFDA.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) 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 ‘spatialFDA/DESCRIPTION’ ... OK * this is package ‘spatialFDA’ version ‘1.1.3’ * 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 ‘spatialFDA’ 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 crossSpatialInference : <anonymous>: no visible binding for global variable ‘continous’ spatialInference: no visible binding for global variable ‘ID’ Undefined global functions or variables: ID continous * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed crossSpatialInference 25.845 1.084 27.422 functionalGam 7.672 0.364 8.332 spatialInference 7.638 0.371 8.311 plotMdl 7.605 0.351 8.193 calcCrossMetricPerFov 7.220 0.447 8.229 plotCrossMetricPerFov 5.744 0.269 6.231 * 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-3.22-bioc/meat/spatialFDA.Rcheck/00check.log’ for details.
spatialFDA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL spatialFDA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘spatialFDA’ ... ** this is package ‘spatialFDA’ version ‘1.1.3’ ** using staged installation ** R ** 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 (spatialFDA)
spatialFDA.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 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(spatialFDA) > > test_check("spatialFDA") imcdatasets not installed. Full functionality, documentation, and loading of data might not be possible without installing loading from cache require("SingleCellExperiment") [1] "Calculating Gest of alpha" [1] "Calculating markcorr of alpha" [1] "Calculating Gcross from alpha to beta" [1] "Calculating Gest of alpha" [1] "Calculating Gcross from alpha to alpha" [1] "Calculating Gcross from beta to alpha" [1] "Calculating Gcross from delta to alpha" [1] "Calculating Gcross from alpha to beta" [1] "Calculating Gcross from beta to beta" [1] "Calculating Gcross from delta to beta" [1] "Calculating Gcross from alpha to delta" [1] "Calculating Gcross from beta to delta" [1] "Calculating Gcross from delta to delta" [1] "alpha" [1] "Calculating Kdot of alpha" [1] "beta" [1] "Calculating Kdot of beta" [1] "delta" [1] "Calculating Kdot of delta" [1] "Calculating Lcross from alpha to Tc" [1] "Calculating Gcross from alpha to Tc" Attaching package: 'tidyr' The following object is masked from 'package:S4Vectors': expand The following object is masked from 'package:testthat': matches Attaching package: 'dplyr' The following object is masked from 'package:Biobase': combine The following objects are masked from 'package:GenomicRanges': intersect, setdiff, union The following object is masked from 'package:Seqinfo': intersect The following objects are masked from 'package:IRanges': collapse, desc, intersect, setdiff, slice, union The following objects are masked from 'package:S4Vectors': first, intersect, rename, setdiff, setequal, union The following objects are masked from 'package:BiocGenerics': combine, intersect, setdiff, setequal, union The following object is masked from 'package:generics': explain The following object is masked from 'package:matrixStats': count The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union imcdatasets not installed. Full functionality, documentation, and loading of data might not be possible without installing loading from cache [1] "Calculating Gest of alpha" [1] "Creating design matrix with Non-diabetic as reference" [1] "Calculating Gcross from alpha to alpha" [1] "Creating design matrix with Non-diabetic as reference" [1] "Calculating Gcross from acinar to alpha" [1] "Creating design matrix with Non-diabetic as reference" [1] "Calculating Gcross from alpha to acinar" [1] "Creating design matrix with Non-diabetic as reference" [1] "Calculating Gcross from acinar to acinar" [1] "Creating design matrix with Non-diabetic as reference" imcdatasets not installed. Full functionality, documentation, and loading of data might not be possible without installing loading from cache [1] "Calculating Gcross from alpha to beta" imcdatasets not installed. Full functionality, documentation, and loading of data might not be possible without installing loading from cache [1] "Calculating Gcross from alpha to beta" imcdatasets not installed. Full functionality, documentation, and loading of data might not be possible without installing loading from cache [1] "Calculating Gcross from alpha to beta" [1] "Calculating Gcross from alpha to beta" [1] "Creating design matrix with Non-diabetic as reference" [ FAIL 0 | WARN 5 | SKIP 0 | PASS 44 ] [ FAIL 0 | WARN 5 | SKIP 0 | PASS 44 ] > > proc.time() user system elapsed 117.116 6.296 126.495
spatialFDA.Rcheck/spatialFDA-Ex.timings
name | user | system | elapsed | |
calcCrossMetricPerFov | 7.220 | 0.447 | 8.229 | |
calcMetricPerFov | 2.963 | 0.161 | 3.340 | |
crossSpatialInference | 25.845 | 1.084 | 27.422 | |
dot-dfToppp | 2.903 | 0.183 | 3.383 | |
dot-extractMetric | 2.828 | 0.159 | 3.184 | |
dot-loadExample | 2.516 | 0.164 | 2.856 | |
dot-speToDf | 2.807 | 0.214 | 3.236 | |
functionalGam | 7.672 | 0.364 | 8.332 | |
functionalPCA | 3.132 | 0.206 | 3.555 | |
plotCrossMetricPerFov | 5.744 | 0.269 | 6.231 | |
plotFbPlot | 3.084 | 0.186 | 3.472 | |
plotFpca | 3.170 | 0.184 | 3.567 | |
plotMdl | 7.605 | 0.351 | 8.193 | |
plotMetricPerFov | 3.177 | 0.208 | 3.750 | |
prepData | 3.026 | 0.166 | 3.424 | |
print.fpca | 3.089 | 0.171 | 3.423 | |
spatialInference | 7.638 | 0.371 | 8.311 | |