| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-22 13:17 -0400 (Tue, 22 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4599 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4553 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4570 |
| 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 24.04.1 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino7 | 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 | | ||||||||
| 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. |
| Package: scRepertoire |
| Version: 2.4.0 |
| 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_2.4.0.tar.gz |
| StartedAt: 2025-04-21 23:26:27 -0400 (Mon, 21 Apr 2025) |
| EndedAt: 2025-04-21 23:35:45 -0400 (Mon, 21 Apr 2025) |
| EllapsedTime: 558.6 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_2.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/scRepertoire.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* 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 ‘2.4.0’
* 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: ‘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 33.843 3.191 37.363
StartracDiversity 6.296 0.355 6.694
* 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-3.21-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 ‘2.4.0’ ** 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 RC (2025-04-04 r88126) -- "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
0.215 0.081 0.290
scRepertoire.Rcheck/tests/testthat.Rout
R version 4.5.0 RC (2025-04-04 r88126) -- "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 0 | SKIP 23 | PASS 98 ]
══ 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 98 ]
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
157.585 6.263 167.173
scRepertoire.Rcheck/scRepertoire-Ex.timings
| name | user | system | elapsed | |
| StartracDiversity | 6.296 | 0.355 | 6.694 | |
| addVariable | 0.886 | 0.035 | 0.927 | |
| alluvialClones | 4.631 | 0.114 | 4.776 | |
| clonalAbundance | 1.614 | 0.037 | 1.663 | |
| clonalBias | 2.090 | 0.079 | 2.183 | |
| clonalCluster | 1.236 | 0.039 | 1.283 | |
| clonalCompare | 1.666 | 0.058 | 1.737 | |
| clonalDiversity | 3.294 | 0.071 | 3.388 | |
| clonalHomeostasis | 1.152 | 0.036 | 1.193 | |
| clonalLength | 1.807 | 0.028 | 1.847 | |
| clonalNetwork | 0.000 | 0.001 | 0.000 | |
| clonalOccupy | 2.637 | 0.068 | 2.726 | |
| clonalOverlap | 1.117 | 0.027 | 1.152 | |
| clonalOverlay | 2.595 | 0.050 | 2.665 | |
| clonalProportion | 1.162 | 0.047 | 1.216 | |
| clonalQuant | 1.241 | 0.033 | 1.288 | |
| clonalRarefaction | 3.373 | 0.081 | 3.479 | |
| clonalScatter | 1.278 | 0.034 | 1.323 | |
| clonalSizeDistribution | 33.843 | 3.191 | 37.363 | |
| combineBCR | 4.110 | 0.096 | 4.545 | |
| combineExpression | 1.623 | 0.058 | 1.699 | |
| combineTCR | 0.946 | 0.035 | 0.992 | |
| createHTOContigList | 0.000 | 0.001 | 0.000 | |
| exportClones | 0.000 | 0.000 | 0.001 | |
| getCirclize | 1.621 | 0.052 | 1.689 | |
| highlightClones | 1.532 | 0.058 | 1.600 | |
| loadContigs | 0.315 | 0.017 | 1.154 | |
| percentAA | 2.592 | 0.059 | 2.670 | |
| percentGenes | 1.402 | 0.043 | 1.453 | |
| percentKmer | 1.846 | 0.036 | 1.892 | |
| percentVJ | 2.659 | 0.062 | 2.736 | |
| positionalEntropy | 1.772 | 0.035 | 1.817 | |
| positionalProperty | 3.743 | 0.078 | 3.838 | |
| quietVDJgenes | 0.137 | 0.004 | 0.141 | |
| subsetClones | 0.986 | 0.032 | 1.023 | |
| vizGenes | 2.133 | 0.069 | 2.211 | |