Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-07 20:24 -0400 (Fri, 07 Jun 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" | 4755 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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: 2.0.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings scRepertoire_2.0.0.tar.gz |
StartedAt: 2024-06-06 03:20:03 -0400 (Thu, 06 Jun 2024) |
EndedAt: 2024-06-06 03:32:20 -0400 (Thu, 06 Jun 2024) |
EllapsedTime: 737.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scRepertoire.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:scRepertoire.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings scRepertoire_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/scRepertoire.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 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 ... 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 28.597 0.252 28.850 combineBCR 14.192 0.180 14.936 StartracDiversity 6.291 0.244 6.535 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/scRepertoire.Rcheck/00check.log’ for details.
scRepertoire.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL scRepertoire ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘scRepertoire’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c aaKmers.cpp -o aaKmers.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c constructConDfAndParseBCR.cpp -o constructConDfAndParseBCR.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c constructConDfAndparseTCR.cpp -o constructConDfAndparseTCR.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c ntKmers.cpp -o ntKmers.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o scRepertoire.so RcppExports.o aaKmers.o constructConDfAndParseBCR.o constructConDfAndparseTCR.o ntKmers.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 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) NULL > > proc.time() user system elapsed 0.191 0.017 0.195
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-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") [ 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 164.209 3.056 170.317
scRepertoire.Rcheck/scRepertoire-Ex.timings
name | user | system | elapsed | |
StartracDiversity | 6.291 | 0.244 | 6.535 | |
addVariable | 1.961 | 0.145 | 2.105 | |
alluvialClones | 3.674 | 0.135 | 3.810 | |
clonalAbundance | 1.562 | 0.035 | 1.598 | |
clonalBias | 1.996 | 0.001 | 1.996 | |
clonalCluster | 4.234 | 0.019 | 4.254 | |
clonalCompare | 1.689 | 0.057 | 1.745 | |
clonalDiversity | 3.262 | 0.064 | 3.327 | |
clonalHomeostasis | 2.226 | 0.076 | 2.301 | |
clonalLength | 1.510 | 0.020 | 1.531 | |
clonalNetwork | 0 | 0 | 0 | |
clonalOccupy | 1.486 | 0.008 | 1.495 | |
clonalOverlap | 1.905 | 0.028 | 1.933 | |
clonalOverlay | 1.567 | 0.008 | 1.575 | |
clonalProportion | 1.055 | 0.000 | 1.055 | |
clonalQuant | 1.146 | 0.004 | 1.149 | |
clonalRarefaction | 3.110 | 0.012 | 3.122 | |
clonalScatter | 1.151 | 0.000 | 1.151 | |
clonalSizeDistribution | 28.597 | 0.252 | 28.850 | |
combineBCR | 14.192 | 0.180 | 14.936 | |
combineExpression | 1.305 | 0.016 | 1.320 | |
combineTCR | 0.841 | 0.000 | 0.842 | |
createHTOContigList | 0 | 0 | 0 | |
exportClones | 0 | 0 | 0 | |
getCirclize | 1.420 | 0.012 | 1.431 | |
highlightClones | 1.329 | 0.000 | 1.329 | |
loadContigs | 0.536 | 0.000 | 1.533 | |
percentAA | 2.232 | 0.004 | 2.237 | |
percentGenes | 1.319 | 0.003 | 1.322 | |
percentKmer | 1.655 | 0.124 | 1.779 | |
percentVJ | 1.711 | 0.116 | 1.827 | |
positionalEntropy | 2.720 | 0.252 | 2.973 | |
positionalProperty | 3.333 | 0.160 | 3.493 | |
subsetClones | 0.842 | 0.052 | 0.894 | |
vizGenes | 1.074 | 0.004 | 1.078 | |