Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-22 12:03 -0400 (Mon, 22 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" | 4814 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
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 1931/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scRepertoire 2.5.3 (landing page) Nick Borcherding
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the scRepertoire package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scRepertoire.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: scRepertoire |
Version: 2.5.3 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scRepertoire_2.5.3.tar.gz |
StartedAt: 2025-09-22 04:06:42 -0400 (Mon, 22 Sep 2025) |
EndedAt: 2025-09-22 04:21:04 -0400 (Mon, 22 Sep 2025) |
EllapsedTime: 861.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: scRepertoire.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scRepertoire_2.5.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scRepertoire.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘scRepertoire/DESCRIPTION’ ... OK * this is package ‘scRepertoire’ version ‘2.5.3’ * 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 ‘scRepertoire’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... INFO installed size is 5.1Mb sub-directories of 1Mb or more: data 2.3Mb libs 2.0Mb * 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 ... NOTE Found the following CITATION file in a non-standard place: CITATION.cff Most likely ‘inst/CITATION’ should be used instead. * 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 whether startup messages can be suppressed ... 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 .calculatePairwiseIndices: no visible global function definition for ‘combn’ clonalSizeDistribution: no visible binding for global variable ‘y’ Undefined global functions or variables: combn y Consider adding importFrom("utils", "combn") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file 'StartracDiversity.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'alluvialClones.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalAbundance.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalBias.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalDiversity.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalHomeostasis.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalLength.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalNetwork.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalOccupy.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalOverlap.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalProportion.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalQuant.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalRarefaction.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalScatter.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'clonalSizeDistribution.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'percentAA.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'percentGeneUsage.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'percentKmer.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'positionalEntropy.Rd': ‘[grDevices:palettes]{hcl.pals}’ Non-topic package-anchored link(s) in Rd file 'positionalProperty.Rd': ‘[grDevices:palettes]{hcl.pals}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed clonalCluster 14.038 0.761 8.345 StartracDiversity 10.428 0.328 10.757 clonalSizeDistribution 9.105 0.081 9.187 percentGeneUsage 6.858 0.041 6.900 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: union [ FAIL 1 | WARN 1 | SKIP 0 | PASS 751 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-clonalScatter.R:76:3'): Plotting output has the correct components ── plot_output$labels$fill (`actual`) not equal to "class" (`expected`). `actual` is NULL `expected` is a character vector ('class') [ FAIL 1 | WARN 1 | SKIP 0 | PASS 751 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 4 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/scRepertoire.Rcheck/00check.log’ for details.
scRepertoire.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scRepertoire ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘scRepertoire’ ... ** this is package ‘scRepertoire’ version ‘2.5.3’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c constructConDfAndParseBCR.cpp -o constructConDfAndParseBCR.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c constructConDfAndparseTCR.cpp -o constructConDfAndparseTCR.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o scRepertoire.so RcppExports.o constructConDfAndParseBCR.o constructConDfAndparseTCR.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-scRepertoire/00new/scRepertoire/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to 'floor' Note: wrong number of arguments to 'floor' ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scRepertoire)
scRepertoire.Rcheck/tests/spelling.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) All Done! > > proc.time() user system elapsed 0.157 0.030 0.175
scRepertoire.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(scRepertoire) Loading required package: ggplot2 > > test_check("scRepertoire") Attaching package: 'igraph' The following object is masked from 'package:testthat': compare The following objects are masked from 'package:stats': decompose, spectrum The following object is masked from 'package:base': union [ FAIL 1 | WARN 1 | SKIP 0 | PASS 751 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-clonalScatter.R:76:3'): Plotting output has the correct components ── plot_output$labels$fill (`actual`) not equal to "class" (`expected`). `actual` is NULL `expected` is a character vector ('class') [ FAIL 1 | WARN 1 | SKIP 0 | PASS 751 ] Error: Test failures Execution halted
scRepertoire.Rcheck/scRepertoire-Ex.timings
name | user | system | elapsed | |
StartracDiversity | 10.428 | 0.328 | 10.757 | |
addVariable | 0.808 | 0.037 | 0.845 | |
alluvialClones | 2.871 | 0.072 | 2.944 | |
annotateInvariant | 1.573 | 0.011 | 1.583 | |
clonalAbundance | 1.700 | 0.014 | 1.713 | |
clonalBias | 2.805 | 0.057 | 2.861 | |
clonalCluster | 14.038 | 0.761 | 8.345 | |
clonalCompare | 2.551 | 0.035 | 2.586 | |
clonalDiversity | 1.774 | 0.046 | 1.820 | |
clonalHomeostasis | 1.146 | 0.003 | 1.150 | |
clonalLength | 1.800 | 0.021 | 1.821 | |
clonalNetwork | 0.001 | 0.000 | 0.000 | |
clonalOccupy | 1.737 | 0.017 | 1.756 | |
clonalOverlap | 1.039 | 0.007 | 1.046 | |
clonalOverlay | 1.897 | 0.009 | 1.906 | |
clonalProportion | 1.143 | 0.000 | 1.143 | |
clonalQuant | 1.229 | 0.000 | 1.229 | |
clonalRarefaction | 4.102 | 0.004 | 4.107 | |
clonalScatter | 1.172 | 0.004 | 1.176 | |
clonalSizeDistribution | 9.105 | 0.081 | 9.187 | |
combineBCR | 4.249 | 0.023 | 1.820 | |
combineExpression | 2.283 | 0.046 | 2.330 | |
combineTCR | 0.779 | 0.000 | 0.779 | |
createHTOContigList | 0 | 0 | 0 | |
exportClones | 0 | 0 | 0 | |
getCirclize | 1.446 | 0.039 | 1.485 | |
highlightClones | 1.268 | 0.000 | 1.269 | |
loadContigs | 0.661 | 0.027 | 1.838 | |
percentAA | 2.261 | 0.043 | 2.305 | |
percentGeneUsage | 6.858 | 0.041 | 6.900 | |
percentKmer | 1.538 | 0.016 | 1.553 | |
positionalEntropy | 1.555 | 0.006 | 1.561 | |
positionalProperty | 2.484 | 0.016 | 2.499 | |
quietVDJgenes | 0.079 | 0.000 | 0.079 | |
subsetClones | 0.865 | 0.000 | 0.866 | |