Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-24 12:08 -0400 (Wed, 24 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4827 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4614 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4558 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4560 |
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 2110/2334 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Statial 1.11.5 (landing page) Farhan Ameen
| 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 | TIMEOUT | ||||||||||
To the developers/maintainers of the Statial package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Statial.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: Statial |
Version: 1.11.5 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:Statial.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Statial_1.11.5.tar.gz |
StartedAt: 2025-09-23 12:35:24 -0000 (Tue, 23 Sep 2025) |
EndedAt: 2025-09-23 13:15:25 -0000 (Tue, 23 Sep 2025) |
EllapsedTime: 2400.2 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: Statial.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:Statial.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings Statial_1.11.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Statial.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 ‘Statial/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Statial’ version ‘1.11.5’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 23 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 ‘Statial’ 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 ... NOTE Namespaces in Imports field not imported from: ‘cluster’ ‘spatstat.explore’ ‘treekoR’ All declared Imports should be used. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.generateBPParam’ ‘.quiet’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .Kontext: no visible binding for global variable ‘cellTypeI’ .Kontext: no visible binding for global variable ‘cellTypeJ’ .Kontext: no visible binding for global variable ‘weightParent’ .Kontext: no visible binding for global variable ‘edge’ .Kontext: no visible binding for global variable ‘i’ .Kontext: no visible binding for global variable ‘j’ .Lfunction: no visible binding for global variable ‘cellTypeI’ .Linhomfunction: no visible binding for global variable ‘cellTypeI’ .Linhomfunction: no visible binding for global variable ‘cellTypeJ’ .Linhomfunction: no visible binding for global variable ‘weightParent’ .Linhomfunction: no visible binding for global variable ‘edge’ .Linhomfunction: no visible binding for global variable ‘i’ .Linhomfunction: no visible binding for global variable ‘j’ Kontextual : <anonymous> : <anonymous>: no visible binding for global variable ‘d’ Kontextual: no visible binding for global variable ‘test’ Kontextual: no visible binding for global variable ‘parent_name’ KontextualCore: no visible global function definition for ‘.’ KontextualCore: no visible binding for global variable ‘i’ KontextualCore: no visible binding for global variable ‘cellTypeI’ KontextualCore: no visible binding for global variable ‘cellTypeJ’ KontextualCore: no visible binding for global variable ‘Kontext’ calcContamination: no visible global function definition for ‘predict’ calcContamination: no visible binding for global variable ‘.’ calcContamination: no visible binding for global variable ‘cellID’ calcStateChanges: no visible binding for global variable ‘indx’ calcStateChanges: no visible binding for global variable ‘primaryCellType’ calcStateChanges: no visible binding for global variable ‘otherCellType’ calcStateChanges: no visible binding for global variable ‘coef’ calcStateChanges: no visible binding for global variable ‘tval’ calcStateChanges: no visible binding for global variable ‘pval’ calcStateChanges: no visible binding for global variable ‘fdr’ calculateChangesMarker : <anonymous> : <anonymous>: no visible global function definition for ‘var’ calculateChangesMarker : <anonymous>: no visible global function definition for ‘pt’ calculateChangesMarker : <anonymous>: no visible global function definition for ‘qnorm’ distanceCalculator: no visible binding for global variable ‘cellType’ distanceCalculator: no visible binding for global variable ‘d’ getMarkerMeans: no visible binding for global variable ‘value’ getParentPhylo: no visible binding for global variable ‘child’ getParentPhylo: no visible binding for global variable ‘parent’ getParentPhylo: no visible binding for global variable ‘children’ kontextCurve: no visible binding for global variable ‘type’ kontextCurve: no visible binding for global variable ‘r’ kontextCurve: no visible binding for global variable ‘original’ kontextCurve: no visible binding for global variable ‘kontextual’ kontextPlot: no visible binding for global variable ‘r’ kontextPlot: no visible binding for global variable ‘kontextualSd’ kontextPlot: no visible binding for global variable ‘originalSd’ kontextPlot: no visible binding for global variable ‘value’ kontextPlot: no visible binding for global variable ‘name’ kontextPlot: no visible binding for global variable ‘lower’ kontextPlot: no visible binding for global variable ‘upper’ parentCombinations: no visible binding for global variable ‘from’ parentCombinations: no visible binding for global variable ‘to’ plotStateChanges: no visible global function definition for ‘lm’ plotStateChanges: no visible global function definition for ‘formula’ plotStateChanges: no visible global function definition for ‘predict’ plotStateChanges: no visible binding for global variable ‘x’ plotStateChanges: no visible binding for global variable ‘y’ plotStateChanges: no visible binding for global variable ‘density’ plotStateChanges: no visible binding for global variable ‘lm’ prepMatrix: no visible binding for global variable ‘imageID’ prepMatrix: no visible binding for global variable ‘kontextual’ prepMatrix: no visible binding for global variable ‘primaryCellType’ prepMatrix: no visible binding for global variable ‘otherCellType’ prepMatrix: no visible binding for global variable ‘marker’ prepMatrix: no visible binding for global variable ‘type’ relabel: no visible binding for global variable ‘cellType’ Undefined global functions or variables: . Kontext cellID cellType cellTypeI cellTypeJ child children coef d density edge fdr formula from i imageID indx j kontextual kontextualSd lm lower marker name original originalSd otherCellType parent parent_name predict primaryCellType pt pval qnorm r test to tval type upper value var weightParent x y Consider adding importFrom("stats", "coef", "density", "formula", "lm", "predict", "pt", "qnorm", "var") 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ...
Statial.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Statial ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘Statial’ ... ** this is package ‘Statial’ version ‘1.11.5’ ** 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 (Statial)
Statial.Rcheck/Statial-Ex.timings
name | user | system | elapsed | |
Kontextual | 2.558 | 0.084 | 2.674 | |
calcContamination | 90.954 | 0.584 | 70.703 | |
calcStateChanges | 7.058 | 0.032 | 9.586 | |
getAbundances | 11.416 | 0.088 | 15.743 | |
getDistances | 10.838 | 0.016 | 14.479 | |
getMarkerMeans | 27.603 | 0.412 | 33.685 | |
isKontextual | 0 | 0 | 0 | |
kontextCurve | 434.674 | 47.522 | 318.345 | |