| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-05-12 11:44 -0400 (Mon, 12 May 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" | 4833 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4575 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4600 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six" | 4554 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4571 |
| 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 | | ||||||||
| 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. |
| 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: 2025-05-09 09:21:26 -0400 (Fri, 09 May 2025) |
| EndedAt: 2025-05-09 09:40:21 -0400 (Fri, 09 May 2025) |
| EllapsedTime: 1135.6 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 71.752 4.017 77.315
StartracDiversity 11.200 0.507 12.427
clonalDiversity 7.864 0.220 8.156
positionalProperty 7.294 0.096 7.683
combineBCR 6.317 0.094 6.744
alluvialClones 6.069 0.113 6.212
clonalRarefaction 6.051 0.129 6.222
percentAA 5.887 0.114 6.135
* 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 Registered S3 method overwritten by 'future': method from all.equal.connection parallelly ** 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
0.358 0.121 0.520
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 2 | 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 2 | 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
332.307 6.867 377.440
scRepertoire.Rcheck/scRepertoire-Ex.timings
| name | user | system | elapsed | |
| StartracDiversity | 11.200 | 0.507 | 12.427 | |
| addVariable | 1.463 | 0.067 | 1.539 | |
| alluvialClones | 6.069 | 0.113 | 6.212 | |
| clonalAbundance | 3.114 | 0.050 | 3.237 | |
| clonalBias | 3.619 | 0.070 | 3.943 | |
| clonalCluster | 2.964 | 0.061 | 3.055 | |
| clonalCompare | 2.623 | 0.065 | 2.693 | |
| clonalDiversity | 7.864 | 0.220 | 8.156 | |
| clonalHomeostasis | 1.861 | 0.039 | 1.908 | |
| clonalLength | 3.508 | 0.040 | 3.560 | |
| clonalNetwork | 0.001 | 0.001 | 0.001 | |
| clonalOccupy | 3.127 | 0.071 | 3.210 | |
| clonalOverlap | 1.879 | 0.037 | 1.924 | |
| clonalOverlay | 3.138 | 0.100 | 3.300 | |
| clonalProportion | 1.956 | 0.043 | 2.025 | |
| clonalQuant | 2.066 | 0.037 | 2.119 | |
| clonalRarefaction | 6.051 | 0.129 | 6.222 | |
| clonalScatter | 2.017 | 0.036 | 2.060 | |
| clonalSizeDistribution | 71.752 | 4.017 | 77.315 | |
| combineBCR | 6.317 | 0.094 | 6.744 | |
| combineExpression | 2.381 | 0.046 | 2.478 | |
| combineTCR | 1.383 | 0.023 | 1.410 | |
| createHTOContigList | 0.000 | 0.001 | 0.001 | |
| exportClones | 0.000 | 0.001 | 0.001 | |
| getCirclize | 2.580 | 0.068 | 2.659 | |
| highlightClones | 2.486 | 0.097 | 2.589 | |
| loadContigs | 0.505 | 0.027 | 1.405 | |
| percentAA | 5.887 | 0.114 | 6.135 | |
| percentGenes | 2.100 | 0.051 | 2.166 | |
| percentKmer | 3.401 | 0.039 | 3.506 | |
| percentVJ | 3.334 | 0.075 | 3.575 | |
| positionalEntropy | 3.511 | 0.040 | 3.700 | |
| positionalProperty | 7.294 | 0.096 | 7.683 | |
| quietVDJgenes | 0.240 | 0.005 | 0.257 | |
| subsetClones | 1.499 | 0.029 | 1.581 | |
| vizGenes | 3.069 | 0.088 | 3.250 | |