Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1903/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
scRepertoire 2.2.1 (landing page) Nick Borcherding
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | 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 | |||||||||
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: 2.2.1 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scRepertoire.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scRepertoire_2.2.1.tar.gz |
StartedAt: 2024-12-20 05:49:55 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:01:17 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 681.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: scRepertoire.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scRepertoire.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings scRepertoire_2.2.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/scRepertoire.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'scRepertoire/DESCRIPTION' ... OK * this is package 'scRepertoire' version '2.2.1' * 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 whether package 'scRepertoire' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.3.0' * 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 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 ... 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/scRepertoire/libs/x64/scRepertoire.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed clonalSizeDistribution 43.39 2.50 45.87 StartracDiversity 8.67 0.34 9.01 clonalDiversity 5.20 0.12 5.35 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/scRepertoire.Rcheck/00check.log' for details.
scRepertoire.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL scRepertoire ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'scRepertoire' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.3.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c aaKmers.cpp -o aaKmers.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c constructConDfAndParseBCR.cpp -o constructConDfAndParseBCR.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c constructConDfAndparseTCR.cpp -o constructConDfAndparseTCR.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lvCompare.cpp -o lvCompare.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ntKmers.cpp -o ntKmers.o g++ -std=gnu++17 -shared -s -static-libgcc -o scRepertoire.dll tmp.def RcppExports.o aaKmers.o constructConDfAndParseBCR.o constructConDfAndparseTCR.o lvCompare.o ntKmers.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-scRepertoire/00new/scRepertoire/libs/x64 ** 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 ** 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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 0.17 0.09 0.59
scRepertoire.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 0 | SKIP 23 | PASS 93 ] ══ 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 0 | SKIP 23 | PASS 93 ] 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 186.68 7.78 197.61
scRepertoire.Rcheck/scRepertoire-Ex.timings
name | user | system | elapsed | |
StartracDiversity | 8.67 | 0.34 | 9.01 | |
addVariable | 3.35 | 0.05 | 3.41 | |
alluvialClones | 4.14 | 0.20 | 4.34 | |
clonalAbundance | 1.75 | 0.08 | 1.83 | |
clonalBias | 2.47 | 0.01 | 2.48 | |
clonalCluster | 1.66 | 0.04 | 1.69 | |
clonalCompare | 2.17 | 0.06 | 2.23 | |
clonalDiversity | 5.20 | 0.12 | 5.35 | |
clonalHomeostasis | 1.26 | 0.07 | 1.33 | |
clonalLength | 2.22 | 0.04 | 2.27 | |
clonalNetwork | 0 | 0 | 0 | |
clonalOccupy | 2.35 | 0.11 | 2.45 | |
clonalOverlap | 1.43 | 0.02 | 1.47 | |
clonalOverlay | 3.21 | 0.06 | 3.26 | |
clonalProportion | 1.39 | 0.03 | 1.43 | |
clonalQuant | 1.17 | 0.03 | 1.20 | |
clonalRarefaction | 4.36 | 0.16 | 4.50 | |
clonalScatter | 1.34 | 0.01 | 1.36 | |
clonalSizeDistribution | 43.39 | 2.50 | 45.87 | |
combineBCR | 3.19 | 0.19 | 3.72 | |
combineExpression | 1.78 | 0.08 | 1.86 | |
combineTCR | 1.20 | 0.02 | 1.22 | |
createHTOContigList | 0 | 0 | 0 | |
exportClones | 0 | 0 | 0 | |
getCirclize | 2.15 | 0.03 | 2.17 | |
highlightClones | 1.93 | 0.03 | 1.97 | |
loadContigs | 0.39 | 0.00 | 0.70 | |
percentAA | 2.93 | 0.05 | 2.99 | |
percentGenes | 1.92 | 0.01 | 1.94 | |
percentKmer | 3.27 | 0.05 | 3.31 | |
percentVJ | 2.22 | 0.09 | 2.32 | |
positionalEntropy | 2.54 | 0.02 | 2.56 | |
positionalProperty | 4.50 | 0.11 | 4.62 | |
subsetClones | 1.21 | 0.00 | 1.21 | |
vizGenes | 1.59 | 0.01 | 1.61 | |