Nick Borcherding
| Snapshot Date: 2025-05-28 13:25 -0400 (Wed, 28 May 2025) |
| git_url: https://git.bioconductor.org/packages/scRepertoire |
| git_branch: devel |
| git_last_commit: 98cb8a6 |
| git_last_commit_date: 2025-05-27 13:36:31 -0400 (Tue, 27 May 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-05-29 12:04 -0400 (Thu, 29 May 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4531 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4569 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4508 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4464 |
| 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 1911/2306 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scRepertoire 2.5.2 (landing page) Nick Borcherding
| 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 | 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: 2.5.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scRepertoire_2.5.2.tar.gz |
| StartedAt: 2025-05-28 23:17:21 -0400 (Wed, 28 May 2025) |
| EndedAt: 2025-05-28 23:26:19 -0400 (Wed, 28 May 2025) |
| EllapsedTime: 537.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scRepertoire.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scRepertoire_2.5.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scRepertoire.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scRepertoire/DESCRIPTION’ ... OK
* this is package ‘scRepertoire’ version ‘2.5.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 34.177 3.715 38.178
StartracDiversity 7.334 0.321 7.716
* 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
‘/Users/biocbuild/bbs-3.22-bioc/meat/scRepertoire.Rcheck/00check.log’
for details.
scRepertoire.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL scRepertoire ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘scRepertoire’ ... ** this is package ‘scRepertoire’ version ‘2.5.2’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c aaKmers.cpp -o aaKmers.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c constructConDfAndParseBCR.cpp -o constructConDfAndParseBCR.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c constructConDfAndparseTCR.cpp -o constructConDfAndparseTCR.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lvCompare.cpp -o lvCompare.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ntKmers.cpp -o ntKmers.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o scRepertoire.so RcppExports.o aaKmers.o constructConDfAndParseBCR.o constructConDfAndparseTCR.o lvCompare.o ntKmers.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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.
> if(requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.183 0.072 0.248
scRepertoire.Rcheck/tests/testthat.Rout
R version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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/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 2 | SKIP 19 | PASS 105 ]
══ Skipped tests (19) ══════════════════════════════════════════════════════════
• On CRAN (19): '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-clonalProportion.R:7:3',
'test-clonalQuant.R:10:2', 'test-clonalScatter.R:5:3',
'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 2 | SKIP 19 | PASS 105 ]
Deleting unused snapshots:
• StartractDiversity/startracdiversity-plot.svg
• 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
• clonalOverlay/clonaloverlay-plot.svg
• clonalProportion/clonalproportion-order-plot.svg
• clonalQuant/clonalquant-order-plot.svg
• clonalQuant/clonalquant-unscaled-plot.svg
• clonalRarefaction/clonalclonalrarefaction-h0-p1-plot.svg
• clonalRarefaction/clonalclonalrarefaction-h1-p2-plot.svg
• clonalRarefaction/clonalclonalrarefaction-h2-p3-plot.svg
• clonalScatter/clonalscatter-raw-plot.svg
• clonalSizeDistribution/clonalsizedistribution-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
121.543 2.729 128.946
scRepertoire.Rcheck/scRepertoire-Ex.timings
| name | user | system | elapsed | |
| StartracDiversity | 7.334 | 0.321 | 7.716 | |
| addVariable | 0.933 | 0.035 | 0.973 | |
| alluvialClones | 3.183 | 0.083 | 3.287 | |
| annotateInvariant | 1.808 | 0.052 | 1.873 | |
| clonalAbundance | 1.804 | 0.039 | 1.850 | |
| clonalBias | 2.191 | 0.065 | 2.272 | |
| clonalCluster | 1.331 | 0.035 | 1.374 | |
| clonalCompare | 1.743 | 0.039 | 1.792 | |
| clonalDiversity | 3.891 | 0.059 | 3.985 | |
| clonalHomeostasis | 2.155 | 0.048 | 2.225 | |
| clonalLength | 1.744 | 0.034 | 1.804 | |
| clonalNetwork | 0.001 | 0.000 | 0.000 | |
| clonalOccupy | 1.743 | 0.045 | 1.799 | |
| clonalOverlap | 1.109 | 0.033 | 1.150 | |
| clonalOverlay | 1.796 | 0.051 | 1.860 | |
| clonalProportion | 2.169 | 0.056 | 2.240 | |
| clonalQuant | 1.234 | 0.032 | 1.280 | |
| clonalRarefaction | 3.542 | 0.102 | 3.675 | |
| clonalScatter | 1.314 | 0.036 | 1.369 | |
| clonalSizeDistribution | 34.177 | 3.715 | 38.178 | |
| combineBCR | 3.423 | 0.103 | 4.244 | |
| combineExpression | 1.636 | 0.081 | 1.727 | |
| combineTCR | 1.044 | 0.023 | 1.075 | |
| createHTOContigList | 0 | 0 | 0 | |
| exportClones | 0.000 | 0.001 | 0.000 | |
| getCirclize | 1.692 | 0.053 | 1.754 | |
| highlightClones | 1.701 | 0.044 | 1.756 | |
| loadContigs | 0.336 | 0.024 | 1.698 | |
| percentAA | 2.761 | 0.068 | 2.841 | |
| percentGenes | 1.504 | 0.030 | 1.549 | |
| percentKmer | 2.629 | 0.073 | 2.719 | |
| percentVJ | 1.839 | 0.045 | 1.899 | |
| positionalEntropy | 1.708 | 0.052 | 1.769 | |
| positionalProperty | 3.709 | 0.074 | 3.803 | |
| quietVDJgenes | 0.154 | 0.005 | 0.160 | |
| subsetClones | 0.994 | 0.028 | 1.032 | |
| vizGenes | 2.153 | 0.058 | 2.224 | |