Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-30 11:35:54 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
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 1918/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scRepertoire 2.0.0 (landing page) Nick Borcherding
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 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: 2.0.0 |
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_2.0.0.tar.gz |
StartedAt: 2024-05-29 23:38:46 -0400 (Wed, 29 May 2024) |
EndedAt: 2024-05-29 23:49:59 -0400 (Wed, 29 May 2024) |
EllapsedTime: 672.2 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_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/scRepertoire.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘scRepertoire/DESCRIPTION’ ... OK * this is package ‘scRepertoire’ version ‘2.0.0’ * 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 38.129 4.111 42.679 combineBCR 18.957 0.351 26.731 StartracDiversity 8.110 0.370 8.558 clonalCluster 5.131 0.109 5.297 * 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-3.19-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 (2024-04-24) -- "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 0.248 0.093 0.341
scRepertoire.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "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 213.341 8.415 227.585
scRepertoire.Rcheck/scRepertoire-Ex.timings
name | user | system | elapsed | |
StartracDiversity | 8.110 | 0.370 | 8.558 | |
addVariable | 1.011 | 0.034 | 1.053 | |
alluvialClones | 4.369 | 0.178 | 4.596 | |
clonalAbundance | 1.968 | 0.055 | 2.052 | |
clonalBias | 3.101 | 0.097 | 3.230 | |
clonalCluster | 5.131 | 0.109 | 5.297 | |
clonalCompare | 1.913 | 0.058 | 1.989 | |
clonalDiversity | 3.897 | 0.106 | 4.038 | |
clonalHomeostasis | 1.278 | 0.037 | 1.325 | |
clonalLength | 1.896 | 0.042 | 1.958 | |
clonalNetwork | 0.000 | 0.001 | 0.001 | |
clonalOccupy | 2.024 | 0.061 | 2.105 | |
clonalOverlap | 2.213 | 0.052 | 2.284 | |
clonalOverlay | 1.912 | 0.044 | 1.975 | |
clonalProportion | 1.305 | 0.035 | 1.356 | |
clonalQuant | 1.330 | 0.045 | 1.390 | |
clonalRarefaction | 3.592 | 0.098 | 3.725 | |
clonalScatter | 1.288 | 0.030 | 1.330 | |
clonalSizeDistribution | 38.129 | 4.111 | 42.679 | |
combineBCR | 18.957 | 0.351 | 26.731 | |
combineExpression | 1.641 | 0.032 | 1.682 | |
combineTCR | 0.970 | 0.060 | 1.064 | |
createHTOContigList | 0.000 | 0.000 | 0.001 | |
exportClones | 0.000 | 0.000 | 0.001 | |
getCirclize | 1.824 | 0.066 | 1.905 | |
highlightClones | 1.674 | 0.056 | 1.753 | |
loadContigs | 0.457 | 0.090 | 1.539 | |
percentAA | 2.800 | 0.073 | 2.895 | |
percentGenes | 1.588 | 0.062 | 1.659 | |
percentKmer | 2.049 | 0.069 | 2.141 | |
percentVJ | 2.168 | 0.074 | 2.270 | |
positionalEntropy | 2.912 | 0.090 | 3.025 | |
positionalProperty | 4.240 | 0.120 | 4.415 | |
subsetClones | 0.933 | 0.029 | 0.971 | |
vizGenes | 2.324 | 0.092 | 2.439 | |