Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 950/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HiCDOC 1.9.2 (landing page) Maigné Élise
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the HiCDOC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiCDOC.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: HiCDOC |
Version: 1.9.2 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HiCDOC.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HiCDOC_1.9.2.tar.gz |
StartedAt: 2024-12-23 22:50:03 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 22:58:40 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 516.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: HiCDOC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HiCDOC.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HiCDOC_1.9.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HiCDOC.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘HiCDOC/DESCRIPTION’ ... OK * this is package ‘HiCDOC’ version ‘1.9.2’ * 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 ‘HiCDOC’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * 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 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 ... NOTE .checkCompartmentAssignment: no visible binding for global variable ‘chromosome’ .checkPca : f: no visible binding for global variable ‘compartment’ .checkResults: no visible binding for global variable ‘assignment.check’ .computePValues: no visible binding for global variable ‘condition’ .computePValues: no visible binding for global variable ‘chromosome’ .computePValues: no visible binding for global variable ‘index’ .computePValues: no visible global function definition for ‘.’ .computePValues: no visible binding for global variable ‘concordance’ .computePValues: no visible binding for global variable ‘condition.1’ .computePValues: no visible binding for global variable ‘condition.2’ .computePValues: no visible binding for global variable ‘concordance.1’ .computePValues: no visible binding for global variable ‘concordance.2’ .computePValues: no visible binding for global variable ‘compartment’ .computePValues: no visible binding for global variable ‘compartment.1’ .computePValues: no visible binding for global variable ‘compartment.2’ .computePValues: no visible binding for global variable ‘H0_value’ .computePValues: no visible binding for global variable ‘difference’ .computePValues : <anonymous>: no visible binding for global variable ‘difference’ .computePValues: no visible binding for global variable ‘pvalue’ .computePValues: no visible binding for global variable ‘pvalue.adjusted’ .computePValues: no visible binding for global variable ‘direction’ .computePca: no visible binding for global variable ‘chromosome’ .computePca: no visible global function definition for ‘.’ .computePca: no visible binding for global variable ‘condition’ .computePca: no visible binding for global variable ‘compartment’ .computePca: no visible binding for global variable ‘centroid’ .computeSelfInteractionRatios: no visible global function definition for ‘.’ .computeSelfInteractionRatios: no visible binding for global variable ‘index’ .computeSelfInteractionRatios: no visible binding for global variable ‘ratio’ .computeSelfInteractionRatios: no visible binding for global variable ‘variable’ .computeSelfInteractionRatios: no visible binding for global variable ‘chromosome’ .computeSelfInteractionRatios: no visible binding for global variable ‘condition’ .determineChromosomeSizes: no visible binding for global variable ‘minIndex’ .determineChromosomeSizes: no visible binding for global variable ‘index’ .determineChromosomeSizes: no visible global function definition for ‘.’ .determineChromosomeSizes: no visible binding for global variable ‘minStart’ .filterWeakPositionsOfChromosome: no visible global function definition for ‘.’ .filterWeakPositionsOfChromosome: no visible binding for global variable ‘index1’ .filterWeakPositionsOfChromosome: no visible binding for global variable ‘index2’ .filterWeakPositionsOfChromosome: no visible binding for global variable ‘value’ .filterWeakPositionsOfChromosome: no visible binding for global variable ‘variable’ .filterWeakPositionsOfChromosome: no visible binding for global variable ‘index’ .formatDetectCompartment: no visible binding for global variable ‘chromosome’ .formatDetectCompartment: no visible global function definition for ‘.’ .formatDetectCompartment: no visible binding for global variable ‘index’ .formatDetectCompartment: no visible binding for global variable ‘condition’ .formatDetectCompartment: no visible binding for global variable ‘compartment’ .formatDetectCompartment: no visible binding for global variable ‘concordance’ .formatDetectCompartment: no visible binding for global variable ‘significance’ .formatDetectCompartment: no visible binding for global variable ‘pvalue.adjusted’ .formatDetectCompartment: no visible binding for global variable ‘condition.1’ .formatDetectCompartment: no visible binding for global variable ‘condition.2’ .formatDetectCompartment: no visible binding for global variable ‘pvalue’ .formatDetectCompartment: no visible binding for global variable ‘direction’ .formatDetectCompartment: no visible binding for global variable ‘centroid.check’ .formatDetectCompartment: no visible binding for global variable ‘PC1.check’ .formatDetectCompartment: no visible binding for global variable ‘assignment.check’ .messageCheck: no visible binding for global variable ‘chromosome’ .normalizeDistanceEffectOfChromosome: no visible binding for global variable ‘value’ .normalizeDistanceEffectOfChromosome: no visible binding for global variable ‘logvalue’ .normalizeDistanceEffectOfChromosome: no visible binding for global variable ‘logdistance’ .normalizeDistanceEffectOfChromosome: no visible binding for global variable ‘bias’ .parseOneCool: no visible binding for global variable ‘chromosome’ .parseOneCool: no visible binding for global variable ‘index’ .parseOneCool: no visible binding for global variable ‘id1’ .parseOneCool: no visible binding for global variable ‘id2’ .parseOneHiCPro: no visible binding for global variable ‘chromosome’ .parseOneHiCPro: no visible binding for global variable ‘index’ .parseOneHiCPro: no visible binding for global variable ‘startIndex’ .parseOneHiCPro: no visible binding for global variable ‘stopIndex’ .plotInteractionsGrid: no visible binding for global variable ‘start1’ .plotInteractionsGrid: no visible binding for global variable ‘start2’ .plotInteractionsWrap: no visible binding for global variable ‘start1’ .plotInteractionsWrap: no visible binding for global variable ‘start2’ .predictCompartmentsAB: no visible binding for global variable ‘offDiagonal’ .predictCompartmentsAB: no visible binding for global variable ‘ratio’ .predictCompartmentsAB: no visible global function definition for ‘.’ .predictCompartmentsAB: no visible binding for global variable ‘chromosome’ .predictCompartmentsAB: no visible binding for global variable ‘cluster’ .predictCompartmentsAB: no visible binding for global variable ‘A’ .predictCompartmentsAB: no visible binding for global variable ‘1’ .predictCompartmentsAB: no visible binding for global variable ‘2’ .predictCompartmentsAB: no visible binding for global variable ‘compartment’ .predictCompartmentsAB: no visible binding for global variable ‘change’ .predictCompartmentsAB: no visible binding for global variable ‘concordance’ .reduceHiCDOCChromosomes: no visible binding for global variable ‘chromosome’ .reduceHiCDOCConditions: no visible binding for global variable ‘condition’ .setFromTabular: no visible binding for global variable ‘chromosome’ .setFromTabular: no visible binding for global variable ‘position 1’ .setFromTabular: no visible binding for global variable ‘position 2’ .setFromTabular: no visible global function definition for ‘.’ .setFromTabular: no visible binding for global variable ‘bin.1’ .setFromTabular: no visible binding for global variable ‘bin.2’ .setFromTabular: no visible binding for global variable ‘variable’ .setFromTabular: no visible binding for global variable ‘indexC’ .setFromTabular: no visible binding for global variable ‘index’ .tieCentroids: no visible binding for global variable ‘cluster’ .tieCentroids: no visible binding for global variable ‘condition’ .tieCentroids: no visible binding for global variable ‘chromosome’ .tieCentroids: no visible global function definition for ‘.’ .tieCentroids: no visible binding for global variable ‘centroid’ .tieCentroids: no visible binding for global variable ‘cluster.1’ .tieCentroids: no visible binding for global variable ‘cluster.2’ .tieCentroids: no visible binding for global variable ‘change’ .tieCentroids: no visible binding for global variable ‘concordance’ .tieCentroids: no visible binding for global variable ‘compartment’ normalizeTechnicalBiases: no visible global function definition for ‘.’ normalizeTechnicalBiases: no visible binding for global variable ‘seqnames1’ normalizeTechnicalBiases: no visible binding for global variable ‘start1’ normalizeTechnicalBiases: no visible binding for global variable ‘start2’ normalizeTechnicalBiases: no visible binding for global variable ‘chromosome’ plotCentroids: no visible binding for global variable ‘PC1’ plotCentroids: no visible binding for global variable ‘PC2’ plotCentroids: no visible binding for global variable ‘compartment’ plotCentroids: no visible binding for global variable ‘condition’ plotCompartments: no visible binding for global variable ‘position’ plotCompartments: no visible binding for global variable ‘compartment’ plotCompartments: no visible binding for global variable ‘condition’ plotConcordanceDifferences: no visible binding for global variable ‘changed’ plotConcordanceDifferences: no visible binding for global variable ‘compartment.1’ plotConcordanceDifferences: no visible binding for global variable ‘compartment.2’ plotConcordanceDifferences: no visible binding for global variable ‘difference’ plotConcordances: no visible binding for global variable ‘condition’ plotConcordances: no visible binding for global variable ‘pvalue.adjusted’ plotConcordances: no visible binding for global variable ‘concordance’ plotInteractions: no visible global function definition for ‘.’ plotInteractions: no visible binding for global variable ‘seqnames1’ plotInteractions: no visible binding for global variable ‘start1’ plotInteractions: no visible binding for global variable ‘start2’ plotInteractions: no visible binding for global variable ‘variable’ plotInteractions: no visible binding for global variable ‘condition’ plotSelfInteractionRatios: no visible global function definition for ‘.’ plotSelfInteractionRatios: no visible binding for global variable ‘condition’ plotSelfInteractionRatios: no visible binding for global variable ‘index’ plotSelfInteractionRatios: no visible binding for global variable ‘compartment’ plotSelfInteractionRatios: no visible binding for global variable ‘ratio’ concordances,HiCDOCDataSet: no visible binding for global variable ‘centroid.check’ concordances,HiCDOCDataSet: no visible binding for global variable ‘PC1.check’ concordances,HiCDOCDataSet: no visible binding for global variable ‘assignment.check’ concordances,HiCDOCDataSet: no visible binding for global variable ‘chromosome’ Undefined global functions or variables: . 1 2 A H0_value PC1 PC1.check PC2 assignment.check bias bin.1 bin.2 centroid centroid.check change changed chromosome cluster cluster.1 cluster.2 compartment compartment.1 compartment.2 concordance concordance.1 concordance.2 condition condition.1 condition.2 difference direction id1 id2 index index1 index2 indexC logdistance logvalue minIndex minStart offDiagonal position position 1 position 2 pvalue pvalue.adjusted ratio seqnames1 significance start1 start2 startIndex stopIndex value variable * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: HiCDOC.Rd: BiocParallel Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 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 HiCDOC 71.328 0.516 71.449 normalizeTechnicalBiases 59.812 0.202 59.829 plotDistanceEffect 14.717 0.426 15.142 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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: 4 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/HiCDOC.Rcheck/00check.log’ for details.
HiCDOC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL HiCDOC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘HiCDOC’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c constrainedClustering.cpp -o constrainedClustering.o g++ -std=gnu++11 -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 -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -DR_NO_REMAP -c parseHiCFile.cpp -o parseHiCFile.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o HiCDOC.so RcppExports.o constrainedClustering.o parseHiCFile.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-HiCDOC/00new/HiCDOC/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (HiCDOC)
HiCDOC.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 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. > library(testthat) > library(HiCDOC) Loading required package: InteractionSet Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > > test_check("HiCDOC") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 334 ] > > proc.time() user system elapsed 45.349 1.527 46.372
HiCDOC.Rcheck/HiCDOC-Ex.timings
name | user | system | elapsed | |
HiCDOC | 71.328 | 0.516 | 71.449 | |
HiCDOCDataSet-methods | 0.091 | 0.002 | 0.094 | |
HiCDOCDataSet-parameters | 0.008 | 0.002 | 0.009 | |
HiCDOCDataSetFromCool | 0.000 | 0.001 | 0.001 | |
HiCDOCDataSetFromHiC | 0.000 | 0.001 | 0.000 | |
HiCDOCDataSetFromHiCPro | 0.000 | 0.001 | 0.000 | |
HiCDOCDataSetFromTabular | 0.174 | 0.001 | 0.169 | |
detectCompartments | 2.611 | 0.088 | 2.540 | |
exampleHiCDOCDataSet | 0.014 | 0.000 | 0.014 | |
exampleHiCDOCDataSetProcessed | 0.016 | 0.004 | 0.020 | |
filterSmallChromosomes | 0.039 | 0.000 | 0.039 | |
filterSparseReplicates | 0.100 | 0.000 | 0.099 | |
filterWeakPositions | 0.503 | 0.004 | 0.394 | |
normalizeBiologicalBiases | 1.726 | 0.003 | 1.621 | |
normalizeDistanceEffect | 2.311 | 0.001 | 2.189 | |
normalizeTechnicalBiases | 59.812 | 0.202 | 59.829 | |
plotCentroids | 0.382 | 0.005 | 0.386 | |
plotCompartmentChanges | 1.344 | 0.024 | 1.368 | |
plotCompartments | 0.329 | 0.001 | 0.330 | |
plotConcordanceDifferences | 0.187 | 0.001 | 0.188 | |
plotConcordances | 0.348 | 0.001 | 0.350 | |
plotDistanceEffect | 14.717 | 0.426 | 15.142 | |
plotInteractions | 0.757 | 0.002 | 0.748 | |
plotSelfInteractionRatios | 0.310 | 0.002 | 0.311 | |
reduceHiCDOCDataSet | 0.033 | 0.000 | 0.033 | |