Nick Borcherding
| Snapshot Date: 2024-05-01 14:05:06 -0400 (Wed, 01 May 2024) |
| git_url: https://git.bioconductor.org/packages/scRepertoire |
| git_branch: devel |
| git_last_commit: 9061c35 |
| git_last_commit_date: 2024-04-30 11:29:08 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-03 11:38:50 -0400 (Fri, 03 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4660 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4391 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4422 |
| 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 1858/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scRepertoire 2.1.0 (landing page) Nick Borcherding
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 2.1.0 |
| 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_2.1.0.tar.gz |
| StartedAt: 2024-05-02 11:13:38 -0400 (Thu, 02 May 2024) |
| EndedAt: 2024-05-02 11:38:58 -0400 (Thu, 02 May 2024) |
| EllapsedTime: 1520.4 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_2.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/scRepertoire.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scRepertoire/DESCRIPTION’ ... OK
* this is package ‘scRepertoire’ version ‘2.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... NOTE
License stub is invalid DCF.
* 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 ... NOTE
checkRd: (-1) percentGenes.Rd:38: Lost braces
38 | examining VJ pairing, please see code{\link{percentVJ}}
| ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 76.935 2.362 95.727
combineBCR 45.034 0.485 53.552
StartracDiversity 11.819 0.546 15.446
clonalCluster 11.782 0.171 14.524
positionalProperty 8.784 0.123 10.366
clonalDiversity 7.743 0.143 9.113
alluvialClones 6.430 0.259 8.221
clonalRarefaction 6.005 0.112 7.173
percentAA 5.250 0.078 6.122
clonalBias 4.755 0.102 6.016
loadContigs 0.510 0.028 7.419
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/Resources/library’ * installing *source* package ‘scRepertoire’ ... ** 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/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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 ntKmers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 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
0.361 0.120 0.479
scRepertoire.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 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")
[ FAIL 0 | WARN 1 | SKIP 23 | PASS 79 ]
══ 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:11:3',
'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 1 | SKIP 23 | PASS 79 ]
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-scaled-plot.svg
• clonalCompare/clonalcompare-area-plot.svg
• clonalCompare/clonalcompare-highlight-relabel-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
• clonalQuant/clonalquant-unscaled-plot.svg
• clonalRarefaction/clonalclonalrarefaction-h1-p2-plot.svg
• clonalRarefaction/clonalclonalrarefaction-h2-p3-plot.svg
• clonalScatter/clonalscatter-raw-plot.svg
• positionalEntropy/positionalentropy-tra-plot.svg
• positionalProperty/positionalentropy-kidera-plot.svg
• positionalProperty/positionalentropy-stscales-plot.svg
• positionalProperty/positionalentropy-tra-plot.svg
• positionalProperty/positionalentropy-tscales-plot.svg
• positionalProperty/positionalentropy-vhse-plot.svg
• vizGenes/vizgenes-heatmap-vignette-plot.svg
>
> proc.time()
user system elapsed
449.201 8.942 560.737
scRepertoire.Rcheck/scRepertoire-Ex.timings
| name | user | system | elapsed | |
| StartracDiversity | 11.819 | 0.546 | 15.446 | |
| addVariable | 2.402 | 0.047 | 3.037 | |
| alluvialClones | 6.430 | 0.259 | 8.221 | |
| clonalAbundance | 3.150 | 0.052 | 3.896 | |
| clonalBias | 4.755 | 0.102 | 6.016 | |
| clonalCluster | 11.782 | 0.171 | 14.524 | |
| clonalCompare | 3.101 | 0.059 | 3.771 | |
| clonalDiversity | 7.743 | 0.143 | 9.113 | |
| clonalHomeostasis | 2.046 | 0.032 | 2.372 | |
| clonalLength | 3.723 | 0.086 | 4.421 | |
| clonalNetwork | 0.000 | 0.001 | 0.001 | |
| clonalOccupy | 4.022 | 0.065 | 4.800 | |
| clonalOverlap | 1.954 | 0.044 | 2.317 | |
| clonalOverlay | 3.153 | 0.051 | 3.724 | |
| clonalProportion | 2.042 | 0.036 | 2.497 | |
| clonalQuant | 3.046 | 0.045 | 3.519 | |
| clonalRarefaction | 6.005 | 0.112 | 7.173 | |
| clonalScatter | 2.053 | 0.036 | 2.468 | |
| clonalSizeDistribution | 76.935 | 2.362 | 95.727 | |
| combineBCR | 45.034 | 0.485 | 53.552 | |
| combineExpression | 2.379 | 0.030 | 2.779 | |
| combineTCR | 1.439 | 0.031 | 1.693 | |
| createHTOContigList | 0.000 | 0.001 | 0.001 | |
| exportClones | 0.000 | 0.001 | 0.001 | |
| getCirclize | 3.019 | 0.038 | 3.623 | |
| highlightClones | 2.560 | 0.063 | 3.015 | |
| loadContigs | 0.510 | 0.028 | 7.419 | |
| percentAA | 5.250 | 0.078 | 6.122 | |
| percentGenes | 2.377 | 0.038 | 2.816 | |
| percentKmer | 3.786 | 0.059 | 4.404 | |
| percentVJ | 3.389 | 0.037 | 3.966 | |
| positionalEntropy | 3.626 | 0.048 | 4.269 | |
| positionalProperty | 8.784 | 0.123 | 10.366 | |
| subsetClones | 1.372 | 0.028 | 1.622 | |
| vizGenes | 2.120 | 0.042 | 2.485 | |