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This page was generated on 2024-05-07 11:32:35 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 965/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HiCDOC 1.6.0 (landing page) Maigné Élise
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the HiCDOC package: - 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: 1.6.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCDOC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCDOC_1.6.0.tar.gz |
StartedAt: 2024-05-06 22:11:46 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 22:14:32 -0400 (Mon, 06 May 2024) |
EllapsedTime: 165.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: HiCDOC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:HiCDOC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings HiCDOC_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/HiCDOC.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-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 Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘HiCDOC/DESCRIPTION’ ... OK * this is package ‘HiCDOC’ version ‘1.6.0’ * 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 ‘HiCDOC’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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’ .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’ .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’ .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 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 H0_value id1 id2 index index1 index2 indexC logdistance logvalue minIndex minStart offDiagonal PC1 PC1.check PC2 position position 1 position 2 pvalue pvalue.adjusted ratio seqnames1 significance start1 start2 startIndex stopIndex value variable * checking Rd files ... NOTE checkRd: (-1) HiCDOC.Rd:28-30: Lost braces in \itemize; meant \describe ? checkRd: (-1) HiCDOC.Rd:31-33: Lost braces in \itemize; meant \describe ? checkRd: (-1) HiCDOC.Rd:34-37: Lost braces in \itemize; meant \describe ? checkRd: (-1) HiCDOC.Rd:42-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) HiCDOC.Rd:45-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) HiCDOC.Rd:48-50: Lost braces in \itemize; meant \describe ? checkRd: (-1) HiCDOC.Rd:55-58: Lost braces in \itemize; meant \describe ? * 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 data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... 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 29.057 1.311 30.390 normalizeTechnicalBiases 25.885 1.510 27.555 plotDistanceEffect 6.576 0.369 6.957 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/HiCDOC.Rcheck/00check.log’ for details.
HiCDOC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL HiCDOC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘HiCDOC’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c constrainedClustering.cpp -o constrainedClustering.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c parseHiCFile.cpp -o parseHiCFile.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o HiCDOC.so RcppExports.o constrainedClustering.o parseHiCFile.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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. > library(testthat) > library(HiCDOC) Loading required package: InteractionSet Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, tapply, union, 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': expand.grid, I, 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 3 | SKIP 0 | PASS 334 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 334 ] > > proc.time() user system elapsed 17.678 0.684 18.371
HiCDOC.Rcheck/HiCDOC-Ex.timings
name | user | system | elapsed | |
HiCDOC | 29.057 | 1.311 | 30.390 | |
HiCDOCDataSet-methods | 0.027 | 0.003 | 0.030 | |
HiCDOCDataSet-parameters | 0.004 | 0.002 | 0.006 | |
HiCDOCDataSetFromCool | 0 | 0 | 0 | |
HiCDOCDataSetFromHiC | 0 | 0 | 0 | |
HiCDOCDataSetFromHiCPro | 0 | 0 | 0 | |
HiCDOCDataSetFromTabular | 0.054 | 0.001 | 0.055 | |
detectCompartments | 0.870 | 0.035 | 0.926 | |
exampleHiCDOCDataSet | 0.005 | 0.001 | 0.007 | |
exampleHiCDOCDataSetProcessed | 0.010 | 0.002 | 0.013 | |
filterSmallChromosomes | 0.014 | 0.002 | 0.016 | |
filterSparseReplicates | 0.035 | 0.003 | 0.039 | |
filterWeakPositions | 0.148 | 0.010 | 0.163 | |
normalizeBiologicalBiases | 0.822 | 0.062 | 0.909 | |
normalizeDistanceEffect | 0.866 | 0.042 | 0.907 | |
normalizeTechnicalBiases | 25.885 | 1.510 | 27.555 | |
plotCentroids | 0.124 | 0.005 | 0.128 | |
plotCompartmentChanges | 0.412 | 0.015 | 0.426 | |
plotCompartments | 0.102 | 0.001 | 0.104 | |
plotConcordanceDifferences | 0.063 | 0.001 | 0.065 | |
plotConcordances | 0.107 | 0.002 | 0.108 | |
plotDistanceEffect | 6.576 | 0.369 | 6.957 | |
plotInteractions | 0.251 | 0.027 | 0.282 | |
plotSelfInteractionRatios | 0.108 | 0.018 | 0.126 | |
reduceHiCDOCDataSet | 0.012 | 0.001 | 0.013 | |