| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-01 11:39 -0400 (Mon, 01 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" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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. |
| Package: scRepertoire |
| Version: 2.4.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scRepertoire_2.4.0.tar.gz |
| StartedAt: 2025-09-01 02:40:26 -0400 (Mon, 01 Sep 2025) |
| EndedAt: 2025-09-01 02:51:42 -0400 (Mon, 01 Sep 2025) |
| EllapsedTime: 675.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: scRepertoire.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scRepertoire_2.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scRepertoire.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 5.0Mb
sub-directories of 1Mb or more:
data 2.3Mb
libs 1.9Mb
* 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 28.716 0.099 28.817
StartracDiversity 6.282 0.290 6.573
* 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 re-building of vignette outputs ... OK
* 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/bbs-3.21-bioc/R/bin/R CMD INSTALL scRepertoire ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘scRepertoire’ ... ** this is package ‘scRepertoire’ version ‘2.4.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c aaKmers.cpp -o aaKmers.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c constructConDfAndParseBCR.cpp -o constructConDfAndParseBCR.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c constructConDfAndparseTCR.cpp -o constructConDfAndparseTCR.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c lvCompare.cpp -o lvCompare.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ntKmers.cpp -o ntKmers.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o scRepertoire.so RcppExports.o aaKmers.o constructConDfAndParseBCR.o constructConDfAndparseTCR.o lvCompare.o ntKmers.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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)
All Done!
>
> proc.time()
user system elapsed
0.152 0.033 0.175
scRepertoire.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 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
136.32 2.08 142.18
scRepertoire.Rcheck/scRepertoire-Ex.timings
| name | user | system | elapsed | |
| StartracDiversity | 6.282 | 0.290 | 6.573 | |
| addVariable | 0.910 | 0.008 | 0.930 | |
| alluvialClones | 2.856 | 0.055 | 2.912 | |
| clonalAbundance | 2.472 | 0.045 | 2.518 | |
| clonalBias | 1.867 | 0.085 | 1.952 | |
| clonalCluster | 1.183 | 0.010 | 1.194 | |
| clonalCompare | 2.635 | 0.010 | 2.645 | |
| clonalDiversity | 3.142 | 0.108 | 3.251 | |
| clonalHomeostasis | 1.116 | 0.020 | 1.136 | |
| clonalLength | 1.639 | 0.004 | 1.643 | |
| clonalNetwork | 0.001 | 0.000 | 0.001 | |
| clonalOccupy | 2.603 | 0.098 | 2.702 | |
| clonalOverlap | 1.073 | 0.000 | 1.073 | |
| clonalOverlay | 1.704 | 0.033 | 1.736 | |
| clonalProportion | 1.066 | 0.009 | 1.075 | |
| clonalQuant | 1.026 | 0.000 | 1.026 | |
| clonalRarefaction | 3.902 | 0.042 | 3.944 | |
| clonalScatter | 1.145 | 0.005 | 1.150 | |
| clonalSizeDistribution | 28.716 | 0.099 | 28.817 | |
| combineBCR | 2.342 | 0.041 | 3.127 | |
| combineExpression | 1.254 | 0.035 | 1.290 | |
| combineTCR | 0.901 | 0.005 | 0.907 | |
| createHTOContigList | 0 | 0 | 0 | |
| exportClones | 0 | 0 | 0 | |
| getCirclize | 1.309 | 0.001 | 1.310 | |
| highlightClones | 1.355 | 0.002 | 1.357 | |
| loadContigs | 0.676 | 0.022 | 1.655 | |
| percentAA | 2.317 | 0.056 | 2.375 | |
| percentGenes | 1.308 | 0.002 | 1.310 | |
| percentKmer | 2.691 | 0.096 | 2.788 | |
| percentVJ | 1.480 | 0.025 | 1.505 | |
| positionalEntropy | 1.713 | 0.004 | 1.717 | |
| positionalProperty | 3.332 | 0.003 | 3.336 | |
| quietVDJgenes | 0.078 | 0.001 | 0.079 | |
| subsetClones | 0.779 | 0.000 | 0.779 | |
| vizGenes | 1.270 | 0.002 | 1.273 | |