| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-25 11:42 -0400 (Thu, 25 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4827 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4608 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4549 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4581 |
| 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 1938/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scRepertoire 2.4.0 (landing page) Nick Borcherding
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / 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: 2.4.0 |
| 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_2.4.0.tar.gz |
| StartedAt: 2025-09-23 14:44:20 -0000 (Tue, 23 Sep 2025) |
| EndedAt: 2025-09-23 14:56:08 -0000 (Tue, 23 Sep 2025) |
| EllapsedTime: 707.8 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_2.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scRepertoire.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scRepertoire/DESCRIPTION’ ... OK
* this is package ‘scRepertoire’ version ‘2.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 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 ‘scRepertoire’ can be installed ... OK
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
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 ... 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 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 ... 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 'percentGenes.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 'percentVJ.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}’
Non-topic package-anchored link(s) in Rd file 'vizGenes.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
clonalSizeDistribution 55.712 0.315 56.139
StartracDiversity 8.109 0.482 8.610
positionalProperty 5.394 0.143 5.552
alluvialClones 5.191 0.100 5.300
clonalRarefaction 5.068 0.048 5.126
clonalDiversity 4.961 0.092 5.064
loadContigs 0.324 0.016 5.266
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.21-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-devel_2025-02-19/site-library’ * installing *source* package ‘scRepertoire’ ... ** this is package ‘scRepertoire’ version ‘2.4.0’ ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c aaKmers.cpp -o aaKmers.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c constructConDfAndParseBCR.cpp -o constructConDfAndParseBCR.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c constructConDfAndparseTCR.cpp -o constructConDfAndparseTCR.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c lvCompare.cpp -o lvCompare.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ntKmers.cpp -o ntKmers.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/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/lib -lR installing to /home/biocbuild/R/R-devel_2025-02-19/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 Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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
0.198 0.032 0.217
scRepertoire.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 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")
Meta data contains an 'ident' column and will likely result
in errors downstream.
[ FAIL 0 | WARN 0 | SKIP 23 | PASS 97 ]
══ 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 97 ]
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
200.557 3.837 219.425
scRepertoire.Rcheck/scRepertoire-Ex.timings
| name | user | system | elapsed | |
| StartracDiversity | 8.109 | 0.482 | 8.610 | |
| addVariable | 1.172 | 0.024 | 1.199 | |
| alluvialClones | 5.191 | 0.100 | 5.300 | |
| clonalAbundance | 2.346 | 0.052 | 2.403 | |
| clonalBias | 2.828 | 0.028 | 2.862 | |
| clonalCluster | 2.787 | 0.060 | 2.851 | |
| clonalCompare | 2.368 | 0.020 | 2.392 | |
| clonalDiversity | 4.961 | 0.092 | 5.064 | |
| clonalHomeostasis | 1.613 | 0.040 | 1.656 | |
| clonalLength | 3.628 | 0.107 | 3.744 | |
| clonalNetwork | 0.000 | 0.000 | 0.001 | |
| clonalOccupy | 2.442 | 0.012 | 2.460 | |
| clonalOverlap | 1.642 | 0.015 | 1.663 | |
| clonalOverlay | 2.534 | 0.004 | 2.544 | |
| clonalProportion | 1.733 | 0.008 | 1.745 | |
| clonalQuant | 1.712 | 0.000 | 1.716 | |
| clonalRarefaction | 5.068 | 0.048 | 5.126 | |
| clonalScatter | 2.821 | 0.112 | 2.939 | |
| clonalSizeDistribution | 55.712 | 0.315 | 56.139 | |
| combineBCR | 3.533 | 0.068 | 4.478 | |
| combineExpression | 1.884 | 0.012 | 1.900 | |
| combineTCR | 1.166 | 0.004 | 1.174 | |
| createHTOContigList | 0 | 0 | 0 | |
| exportClones | 0 | 0 | 0 | |
| getCirclize | 2.132 | 0.020 | 2.156 | |
| highlightClones | 1.945 | 0.020 | 1.971 | |
| loadContigs | 0.324 | 0.016 | 5.266 | |
| percentAA | 3.465 | 0.116 | 3.590 | |
| percentGenes | 1.815 | 0.116 | 1.935 | |
| percentKmer | 3.609 | 0.251 | 3.871 | |
| percentVJ | 2.278 | 0.120 | 2.404 | |
| positionalEntropy | 2.586 | 0.088 | 2.680 | |
| positionalProperty | 5.394 | 0.143 | 5.552 | |
| quietVDJgenes | 0.122 | 0.008 | 0.130 | |
| subsetClones | 1.280 | 0.040 | 1.321 | |
| vizGenes | 2.845 | 0.120 | 2.970 | |