Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 1903/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scRepertoire 2.2.1 (landing page) Nick Borcherding
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 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 | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: scRepertoire |
Version: 2.2.1 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scRepertoire_2.2.1.tar.gz |
StartedAt: 2024-11-20 12:17:31 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 12:28:57 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 686.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scRepertoire.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scRepertoire_2.2.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scRepertoire.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scRepertoire/DESCRIPTION’ ... OK * this is package ‘scRepertoire’ version ‘2.2.1’ * 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++ (conda-forge gcc 14.2.0-1) 14.2.0’ * checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: data 2.5Mb libs 3.5Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 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 ... OK * 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 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 clonalSizeDistribution 51.437 0.320 51.853 StartracDiversity 8.912 0.247 9.178 positionalProperty 6.464 0.083 6.564 clonalDiversity 5.697 0.136 5.844 clonalRarefaction 5.682 0.072 5.766 loadContigs 0.374 0.013 5.405 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/scRepertoire.Rcheck/00check.log’ for details.
scRepertoire.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL scRepertoire ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘scRepertoire’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c aaKmers.cpp -o aaKmers.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c constructConDfAndParseBCR.cpp -o constructConDfAndParseBCR.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c constructConDfAndparseTCR.cpp -o constructConDfAndparseTCR.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c lvCompare.cpp -o lvCompare.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -c ntKmers.cpp -o ntKmers.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o scRepertoire.so RcppExports.o aaKmers.o constructConDfAndParseBCR.o constructConDfAndparseTCR.o lvCompare.o ntKmers.o -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-scRepertoire/00new/scRepertoire/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** 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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.287 0.023 0.207
scRepertoire.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(scRepertoire) Loading required package: ggplot2 > > test_check("scRepertoire") [ FAIL 0 | WARN 0 | SKIP 23 | PASS 93 ] ══ Skipped tests (23) ══════════════════════════════════════════════════════════ • On CRAN (23): 'test-StartractDiversity.R:10:3', 'test-alluvialClones.R:10:3', 'test-clonalAbundance.R:4:3', 'test-clonalCompare.R:7:3', 'test-clonalDiversity.R:8:3', 'test-clonalHomeostasis.R:7:3', 'test-clonalLength.R:4:3', 'test-clonalNetwork.R:9:3', 'test-clonalOccupy.R:8:3', 'test-clonalOverlap.R:7:3', 'test-clonalOverlay.R:10:3', 'test-clonalProportion.R:7:3', 'test-clonalQuant.R:10:2', 'test-clonalRarefaction.R:9:3', 'test-clonalScatter.R:5:3', 'test-clonalSizeDistribution.R:7:3', 'test-percentAA.R:8:3', 'test-percentGenes.R:8:3', 'test-percentKmer.R:26:3', 'test-percentVJ.R:8:3', 'test-positionalEntropy.R:6:3', 'test-positionalProperty.R:6:3', 'test-vizGenes.R:7:3' [ FAIL 0 | WARN 0 | SKIP 23 | PASS 93 ] Deleting unused snapshots: • alluvialClones/alluvialclones-alpha-plot.svg • alluvialClones/alluvialclones-alphapluscolor-plot.svg • alluvialClones/alluvialclones-facet-plot.svg • alluvialClones/alluvialclones-nocolor-plot.svg • alluvialClones/alluvialclones-trb-plot.svg • clonalAbundance/clonalabundance-group-plot.svg • clonalAbundance/clonalabundance-order-plot.svg • clonalAbundance/clonalabundance-scaled-plot.svg • clonalCompare/clonalcompare-alluvial-order-plot.svg • clonalCompare/clonalcompare-area-plot.svg • clonalCompare/clonalcompare-highlight-relabel-plot.svg • clonalHomeostasis/clonalhomeostasis-order-plot.svg • clonalLength/clonallength-both-chain-order-plot.svg • clonalLength/clonallength-groupby-plot.svg • clonalLength/clonallength-scaled-plot.svg • clonalLength/clonallength-tra-plot.svg • clonalLength/clonallength-trb-plot.svg • clonalNetwork/clonalnetwork-filterclones-1-plot.svg • clonalOccupy/clonaloccupy-proportion-plot.svg • clonalOverlap/clonaloverlap-cosine-plot.svg • clonalOverlap/clonaloverlap-coverlap-plot.svg • clonalOverlap/clonaloverlap-jaccard-plot.svg • clonalOverlap/clonaloverlap-morisita-plot.svg • clonalOverlap/clonaloverlap-order-plot.svg • clonalOverlap/clonaloverlap-reorder-plot.svg • clonalOverlay/clonaloverlay-clonalproportion-plot.svg • clonalProportion/clonalproportion-order-plot.svg • clonalQuant/clonalquant-order-plot.svg • clonalQuant/clonalquant-unscaled-plot.svg • clonalRarefaction/clonalclonalrarefaction-h1-p2-plot.svg • clonalRarefaction/clonalclonalrarefaction-h2-p3-plot.svg • clonalScatter/clonalscatter-raw-plot.svg • percentAA/percentaa-plot.svg • percentGenes/percentgenes-order-plot.svg • percentKmer/percentkmer-group-motif2-order-plot.svg • percentVJ/percentvj-order-plot.svg • positionalEntropy/positionalentropy-tra-plot.svg • positionalEntropy/positionalentropy-trb-order-plot.svg • positionalProperty/positionalentropy-kidera-plot.svg • positionalProperty/positionalentropy-stscales-plot.svg • positionalProperty/positionalentropy-tra-plot.svg • positionalProperty/positionalentropy-trb-order-plot.svg • positionalProperty/positionalentropy-tscales-plot.svg • positionalProperty/positionalentropy-vhse-plot.svg • vizGenes/vizgenes-heatmap-vignette-plot.svg > > proc.time() user system elapsed 204.245 2.314 218.562
scRepertoire.Rcheck/scRepertoire-Ex.timings
name | user | system | elapsed | |
StartracDiversity | 8.912 | 0.247 | 9.178 | |
addVariable | 2.164 | 0.024 | 2.192 | |
alluvialClones | 3.868 | 0.100 | 3.975 | |
clonalAbundance | 2.070 | 0.020 | 2.095 | |
clonalBias | 2.694 | 0.012 | 2.712 | |
clonalCluster | 1.565 | 0.004 | 1.573 | |
clonalCompare | 2.373 | 0.016 | 2.394 | |
clonalDiversity | 5.697 | 0.136 | 5.844 | |
clonalHomeostasis | 1.433 | 0.024 | 1.460 | |
clonalLength | 2.438 | 0.023 | 2.467 | |
clonalNetwork | 0 | 0 | 0 | |
clonalOccupy | 2.304 | 0.004 | 2.313 | |
clonalOverlap | 1.478 | 0.012 | 1.493 | |
clonalOverlay | 2.269 | 0.012 | 2.285 | |
clonalProportion | 1.597 | 0.004 | 1.603 | |
clonalQuant | 1.500 | 0.004 | 1.507 | |
clonalRarefaction | 5.682 | 0.072 | 5.766 | |
clonalScatter | 1.514 | 0.016 | 1.532 | |
clonalSizeDistribution | 51.437 | 0.320 | 51.853 | |
combineBCR | 3.506 | 0.020 | 3.748 | |
combineExpression | 1.800 | 0.008 | 1.812 | |
combineTCR | 1.107 | 0.016 | 1.125 | |
createHTOContigList | 0 | 0 | 0 | |
exportClones | 0 | 0 | 0 | |
getCirclize | 1.919 | 0.000 | 1.921 | |
highlightClones | 2.891 | 0.035 | 2.933 | |
loadContigs | 0.374 | 0.013 | 5.405 | |
percentAA | 3.254 | 0.004 | 3.266 | |
percentGenes | 1.578 | 0.012 | 1.595 | |
percentKmer | 2.369 | 0.016 | 2.392 | |
percentVJ | 2.391 | 0.020 | 2.422 | |
positionalEntropy | 2.347 | 0.012 | 2.370 | |
positionalProperty | 6.464 | 0.083 | 6.564 | |
subsetClones | 1.113 | 0.004 | 1.119 | |
vizGenes | 1.564 | 0.004 | 1.573 | |