Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 1114/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MAGAR 1.13.0 (landing page) Michael Scherer
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the MAGAR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MAGAR.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: MAGAR |
Version: 1.13.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAGAR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MAGAR_1.13.0.tar.gz |
StartedAt: 2024-06-10 04:42:03 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 04:53:42 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 699.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MAGAR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAGAR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MAGAR_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/MAGAR.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'MAGAR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'MAGAR' version '1.13.0' * 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 ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. * checking for portable file names ... OK * checking whether package 'MAGAR' can be installed ... OK * 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 ... NOTE Namespace in Imports field not imported from: 'RnBeads.hg38' All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE getOverlapUniverse: warning in overlapQTLs(meth.qtl.res = meth.qtl.res, type = type): partial argument match of 'meth.qtl.res' to 'meth.qtl.result.list' doGenoImport: no visible global function definition for 'makeGRangesFromDataFrame' doGenoImport: no visible global function definition for 'seqlevelsStyle<-' doGenoImport: no visible global function definition for 'findOverlaps' doGenoImport: no visible global function definition for 'ggplot' doGenoImport: no visible global function definition for 'aes' doGenoImport: no visible binding for global variable 'PC1' doGenoImport: no visible binding for global variable 'PC2' doGenoImport: no visible global function definition for 'geom_point' doGenoImport: no visible global function definition for 'xlab' doGenoImport: no visible global function definition for 'ylab' doGenoImport: no visible global function definition for 'theme_bw' doGenoImport: no visible global function definition for 'theme' doGenoImport: no visible global function definition for 'element_blank' doGenoImport: no visible global function definition for 'element_text' doGenoImport: no visible global function definition for 'element_line' doGenoImport: no visible global function definition for 'ggsave' doGenoImportIDAT: no visible global function definition for 'featureData' doGenoImportIDAT: no visible global function definition for 'featureNames' doGenoImportIDAT: no visible global function definition for 'chromosome' doGenoImportIDAT: no visible global function definition for 'calls' doGenoImportIDAT: no visible global function definition for 'makeGRangesFromDataFrame' doGenoImportIDAT: no visible global function definition for 'GRanges' doGenoImportIDAT: no visible global function definition for 'Rle' doGenoImportIDAT: no visible global function definition for 'IRanges' doGenoImportIDAT: no visible global function definition for 'findOverlaps' doGenoImportIDAT: no visible global function definition for 'queryHits' doGenoImportIDAT: no visible global function definition for 'subjectHits' doGenoImportImputed: no visible global function definition for 'ggplot' doGenoImportImputed: no visible global function definition for 'aes' doGenoImportImputed: no visible binding for global variable 'PC1' doGenoImportImputed: no visible binding for global variable 'PC2' doGenoImportImputed: no visible global function definition for 'geom_point' doGenoImportImputed: no visible global function definition for 'xlab' doGenoImportImputed: no visible global function definition for 'ylab' doGenoImportImputed: no visible global function definition for 'theme_bw' doGenoImportImputed: no visible global function definition for 'theme' doGenoImportImputed: no visible global function definition for 'element_blank' doGenoImportImputed: no visible global function definition for 'element_text' doGenoImportImputed: no visible global function definition for 'element_line' doGenoImportImputed: no visible global function definition for 'ggsave' doImport: no visible binding for global variable 'anno' doMethImport: no visible global function definition for 'GRanges' doMethImport: no visible global function definition for 'Rle' doMethImport: no visible global function definition for 'IRanges' doMethImport: no visible global function definition for 'makeGRangesFromDataFrame' doMethImport: no visible global function definition for 'findOverlaps' doMethImport: no visible global function definition for 'queryHits' doMethQTLChromosome: no visible global function definition for 'ggplot' doMethQTLChromosome: no visible global function definition for 'aes' doMethQTLChromosome: no visible binding for global variable 'Size' doMethQTLChromosome: no visible global function definition for 'after_stat' doMethQTLChromosome: no visible global function definition for 'geom_histogram' doMethQTLChromosome: no visible global function definition for 'geom_vline' doMethQTLChromosome: no visible global function definition for 'theme_bw' doMethQTLChromosome: no visible global function definition for 'theme' doMethQTLChromosome: no visible global function definition for 'element_blank' doMethQTLChromosome: no visible global function definition for 'element_text' doMethQTLChromosome: no visible global function definition for 'element_line' doMethQTLChromosome: no visible global function definition for 'ggsave' doMethQTLChromosome: no visible global function definition for 'mclapply' getOverlapUniverse: no visible global function definition for 'makeGRangesFromDataFrame' qtlAnnotationEnrichment: no visible global function definition for 'findOverlaps' qtlCorrelateCorBlockStat: no visible global function definition for 'ggplot' qtlCorrelateCorBlockStat: no visible global function definition for 'aes_string' qtlCorrelateCorBlockStat: no visible global function definition for 'geom_point' qtlCorrelateCorBlockStat: no visible global function definition for 'geom_smooth' qtlCorrelateCorBlockStat: no visible global function definition for 'ggtitle' qtlCorrelateCorBlockStat: no visible global function definition for 'ylab' qtlDistanceScatterplot: no visible global function definition for 'ggplot' qtlDistanceScatterplot: no visible global function definition for 'aes' qtlDistanceScatterplot: no visible binding for global variable 'Distance' qtlDistanceScatterplot: no visible binding for global variable 'P.value' qtlDistanceScatterplot: no visible global function definition for 'geom_point' qtlDistanceScatterplot: no visible global function definition for 'ggtitle' qtlDistanceScatterplot: no visible global function definition for 'xlab' qtlDistanceScatterplot: no visible global function definition for 'ylab' qtlDistanceScatterplot: no visible binding for global variable 'Beta' qtlDistanceScatterplot: no visible global function definition for 'labs' qtlDistanceScatterplot: no visible global function definition for 'scale_color_gradient2' qtlDistanceScatterplot: no visible global function definition for 'scale_color_continuous' qtlDistanceScatterplot: no visible global function definition for 'annotate' qtlDistanceScatterplot: no visible global function definition for 'ggsave' qtlLOLAEnrichment: no visible global function definition for 'loadRegionDB' qtlLOLAEnrichment: no visible global function definition for 'runLOLA' qtlPlotAnnotationEnrichment: no visible global function definition for 'ggplot' qtlPlotAnnotationEnrichment: no visible global function definition for 'aes' qtlPlotAnnotationEnrichment: no visible binding for global variable 'Type' qtlPlotAnnotationEnrichment: no visible binding for global variable 'Annotation' qtlPlotAnnotationEnrichment: no visible binding for global variable 'OddsRatio' qtlPlotAnnotationEnrichment: no visible global function definition for 'geom_tile' qtlPlotAnnotationEnrichment: no visible global function definition for 'scale_fill_gradient2' qtlPlotBaseSubstitution: no visible global function definition for 'ggplot' qtlPlotBaseSubstitution: no visible global function definition for 'aes' qtlPlotBaseSubstitution: no visible binding for global variable 'Substitution' qtlPlotBaseSubstitution: no visible binding for global variable 'OddsRatio' qtlPlotBaseSubstitution: no visible global function definition for 'geom_tile' qtlPlotBaseSubstitution: no visible global function definition for 'scale_fill_gradient2' qtlPlotClusterSize: no visible global function definition for 'ggplot' qtlPlotClusterSize: no visible global function definition for 'aes' qtlPlotClusterSize: no visible binding for global variable 'Size' qtlPlotClusterSize: no visible global function definition for 'after_stat' qtlPlotClusterSize: no visible global function definition for 'geom_histogram' qtlPlotSNPCorrelationBlock: no visible global function definition for 'ggplot' qtlPlotSNPCorrelationBlock: no visible global function definition for 'aes' qtlPlotSNPCorrelationBlock: no visible binding for global variable 'SNP' qtlPlotSNPCorrelationBlock: no visible binding for global variable 'CpG' qtlPlotSNPCorrelationBlock: no visible global function definition for 'geom_point' qtlPlotSNPCorrelationBlock: no visible binding for global variable 'Representative' qtlPlotSNPCorrelationBlock: no visible global function definition for 'geom_smooth' qtlPlotSNPCorrelationBlock: no visible global function definition for 'facet_grid' qtlPlotSNPCorrelationBlock: no visible global function definition for 'theme' qtlPlotSNPCorrelationBlock: no visible global function definition for 'scale_color_manual' qtlPlotSNPCpGInteraction: no visible global function definition for 'ggplot' qtlPlotSNPCpGInteraction: no visible global function definition for 'aes' qtlPlotSNPCpGInteraction: no visible binding for global variable 'SNP' qtlPlotSNPCpGInteraction: no visible binding for global variable 'CpG' qtlPlotSNPCpGInteraction: no visible global function definition for 'geom_boxplot' qtlPlotSNPCpGInteraction: no visible global function definition for 'theme_bw' qtlPlotSNPCpGInteraction: no visible global function definition for 'ylab' qtlPlotSNPCpGInteraction: no visible global function definition for 'xlab' qtlPlotSNPCpGInteraction: no visible global function definition for 'ggsave' qtlPlotSNPCpGInteraction: no visible binding for global variable 'SNPDosage' qtlPlotSNPCpGInteraction: no visible global function definition for 'geom_point' qtlPlotSNPCpGInteraction: no visible global function definition for 'geom_smooth' Undefined global functions or variables: Annotation Beta CpG Distance GRanges IRanges OddsRatio P.value PC1 PC2 Representative Rle SNP SNPDosage Size Substitution Type aes aes_string after_stat anno annotate calls chromosome element_blank element_line element_text facet_grid featureData featureNames findOverlaps geom_boxplot geom_histogram geom_point geom_smooth geom_tile geom_vline ggplot ggsave ggtitle labs loadRegionDB makeGRangesFromDataFrame mclapply queryHits runLOLA scale_color_continuous scale_color_gradient2 scale_color_manual scale_fill_gradient2 seqlevelsStyle<- subjectHits theme theme_bw xlab ylab * 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 files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed doMethQTL 11.01 0.98 14.50 doMethQTLChromosome 9.32 0.60 11.87 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.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 'F:/biocbuild/bbs-3.20-bioc/meat/MAGAR.Rcheck/00check.log' for details.
MAGAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MAGAR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'MAGAR' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' ** testing if installed package can be loaded from final location No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' ** testing if installed package keeps a record of temporary installation path * DONE (MAGAR)
MAGAR.Rcheck/tests/runTests.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 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. > BiocGenerics:::testPackage("MAGAR") 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, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min 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 Attaching package: 'S4Vectors' The following objects are masked from 'package:Matrix': expand, unname The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'S4Arrays' The following object is masked from 'package:abind': abind The following object is masked from 'package:base': rowsum Attaching package: 'DelayedArray' The following objects are masked from 'package:base': apply, scale, sweep Attaching package: 'HDF5Array' The following object is masked from 'package:rhdf5': h5ls Attaching package: 'bit' The following object is masked from 'package:base': xor Attaching package ff - getOption("fftempdir")=="F:/biocbuild/bbs-3.20-bioc/tmpdir/RtmpmmnbZw/ff" - getOption("ffextension")=="ff" - getOption("ffdrop")==TRUE - getOption("fffinonexit")==TRUE - getOption("ffpagesize")==65536 - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system Attaching package: 'ff' The following object is masked from 'package:S4Arrays': maxlength The following objects are masked from 'package:utils': write.csv, write.csv2 The following objects are masked from 'package:base': is.factor, is.ordered Spam version 2.10-0 (2023-10-23) is loaded. Type 'help( Spam)' or 'demo( spam)' for a short introduction and overview of this package. Help for individual functions is also obtained by adding the suffix '.spam' to the function name, e.g. 'help( chol.spam)'. Attaching package: 'spam' The following object is masked from 'package:Matrix': det The following object is masked from 'package:stats4': mle The following objects are masked from 'package:base': backsolve, forwardsolve Try help(fields) to get started. Attaching package: 'gplots' The following object is masked from 'package:IRanges': space The following object is masked from 'package:S4Vectors': space The following object is masked from 'package:stats': lowess Attaching package: 'grid' The following object is masked from 'package:ff': pattern Attaching package: 'gridExtra' The following object is masked from 'package:BiocGenerics': combine Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA 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:SparseArray': rowMedians The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'AnnotationDbi' The following object is masked from 'package:MASS': select Attaching package: 'Biostrings' The following object is masked from 'package:grid': pattern The following objects are masked from 'package:ff': mismatch, pattern The following object is masked from 'package:base': strsplit locfit 1.5-9.9 2024-03-01 Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Attaching package: 'plyr' The following object is masked from 'package:XVector': compact The following object is masked from 'package:IRanges': desc The following object is masked from 'package:S4Vectors': rename The following object is masked from 'package:matrixStats': count Welcome to oligoClasses version 1.67.0 Attaching package: 'oligoClasses' The following object is masked from 'package:minfi': getM No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' Welcome to crlmm version 1.63.0 Attaching package: 'MAGAR' The following object is masked from 'package:foreach': getResult 2024-06-10 04:53:06 Inf STATUS STARTED Unit Testing 2024-06-10 04:53:06 Inf STATUS STARTED Testing constructors Object of class MethQTLInput Contains 3 samples Methylation data for 5 CpGs Genotyping data for 4 SNPs Genome assembly: hg19 Object of class MethQTLResult Contains 10 methQTL Contains 0 correlation blocks methQTL called using classical.linear representative CpGs computed with row.medians 2024-06-10 04:53:06 Inf STATUS COMPLETED Testing constructors 2024-06-10 04:53:06 Inf STATUS STARTED Testing options 2024-06-10 04:53:06 Inf STATUS COMPLETED Testing options 2024-06-10 04:53:06 Inf STATUS STARTED Testing cor blocks 2024-06-10 04:53:07 Inf STATUS STARTED Compute correlation blocks 2024-06-10 04:53:07 Inf STATUS STARTED Compute correlation matrix 2024-06-10 04:53:07 Inf STATUS COMPLETED Compute correlation matrix 2024-06-10 04:53:07 Inf STATUS STARTED Compute pairwise distances 2024-06-10 04:53:08 Inf STATUS COMPLETED Compute pairwise distances 2024-06-10 04:53:09 Inf STATUS STARTED Weight distances 2024-06-10 04:53:09 Inf STATUS COMPLETED Weight distances 2024-06-10 04:53:10 Inf STATUS STARTED Compute graph 2024-06-10 04:53:10 Inf STATUS COMPLETED Compute graph 2024-06-10 04:53:10 Inf STATUS STARTED Compute clustering 2024-06-10 04:53:11 Inf STATUS COMPLETED Compute clustering 2024-06-10 04:53:11 Inf STATUS COMPLETED Compute correlation blocks 2024-06-10 04:53:11 Inf STATUS COMPLETED Testing cor blocks 2024-06-10 04:53:11 Inf STATUS STARTED Test methQTL calling 2024-06-10 04:53:12 Inf INFO Loading default option setting 2024-06-10 04:53:12 Inf STATUS STARTED Imputation procedure knn 2024-06-10 04:53:12 Inf STATUS COMPLETED Imputation procedure knn 2024-06-10 04:53:12 Inf STATUS STARTED Computing methQTLs 2024-06-10 04:53:12 Inf STATUS STARTED Computing methQTL for chromosome chr18 2024-06-10 04:53:12 Inf STATUS STARTED Compute methQTL per correlation block 2024-06-10 04:53:12 Inf STATUS STARTED Setting up Multicore 2024-06-10 04:53:14 Inf INFO Using 1 cores 2024-06-10 04:53:14 Inf STATUS COMPLETED Setting up Multicore 2024-06-10 04:53:15 Inf STATUS COMPLETED Compute methQTL per correlation block 2024-06-10 04:53:15 Inf STATUS COMPLETED Computing methQTL for chromosome chr18 2024-06-10 04:53:16 Inf STATUS COMPLETED Computing methQTLs 2024-06-10 04:53:16 Inf STATUS COMPLETED Test methQTL calling 2024-06-10 04:53:16 Inf STATUS COMPLETED Unit Testing Object of class MethQTLInput Contains 3 samples Methylation data for 5 CpGs Genotyping data for 4 SNPs Genome assembly: hg19 Object of class MethQTLResult Contains 10 methQTL Contains 0 correlation blocks methQTL called using classical.linear representative CpGs computed with row.medians 2024-06-10 04:53:16 Inf INFO Loading default option setting 2024-06-10 04:53:16 Inf STATUS STARTED Imputation procedure knn 2024-06-10 04:53:16 Inf STATUS COMPLETED Imputation procedure knn 2024-06-10 04:53:16 Inf STATUS STARTED Computing methQTLs 2024-06-10 04:53:16 Inf STATUS STARTED Computing methQTL for chromosome chr18 2024-06-10 04:53:16 Inf STATUS STARTED Compute methQTL per correlation block 2024-06-10 04:53:16 Inf STATUS STARTED Setting up Multicore 2024-06-10 04:53:18 Inf INFO Using 1 cores 2024-06-10 04:53:18 Inf STATUS COMPLETED Setting up Multicore 2024-06-10 04:53:19 Inf STATUS COMPLETED Compute methQTL per correlation block 2024-06-10 04:53:19 Inf STATUS COMPLETED Computing methQTL for chromosome chr18 2024-06-10 04:53:20 Inf STATUS COMPLETED Computing methQTLs 2024-06-10 04:53:20 Inf STATUS STARTED Compute correlation blocks 2024-06-10 04:53:20 Inf STATUS STARTED Compute correlation matrix 2024-06-10 04:53:20 Inf STATUS COMPLETED Compute correlation matrix 2024-06-10 04:53:20 Inf STATUS STARTED Compute pairwise distances 2024-06-10 04:53:22 Inf STATUS COMPLETED Compute pairwise distances 2024-06-10 04:53:23 Inf STATUS STARTED Weight distances 2024-06-10 04:53:23 Inf STATUS COMPLETED Weight distances 2024-06-10 04:53:24 Inf STATUS STARTED Compute graph 2024-06-10 04:53:24 Inf STATUS COMPLETED Compute graph 2024-06-10 04:53:24 Inf STATUS STARTED Compute clustering 2024-06-10 04:53:25 Inf STATUS COMPLETED Compute clustering 2024-06-10 04:53:25 Inf STATUS COMPLETED Compute correlation blocks RUNIT TEST PROTOCOL -- Mon Jun 10 04:53:25 2024 *********************************************** Number of test functions: 4 Number of errors: 0 Number of failures: 0 1 Test Suite : MAGAR RUnit Tests - 4 test functions, 0 errors, 0 failures Number of test functions: 4 Number of errors: 0 Number of failures: 0 There were 50 or more warnings (use warnings() to see the first 50) > > proc.time() user system elapsed 33.20 14.12 51.86
MAGAR.Rcheck/MAGAR-Ex.timings
name | user | system | elapsed | |
computeCorrelationBlocks | 4.81 | 0.12 | 5.00 | |
doImport | 0.05 | 0.02 | 0.06 | |
doMethQTL | 11.01 | 0.98 | 14.50 | |
doMethQTLChromosome | 9.32 | 0.60 | 11.87 | |
filterPval | 0.01 | 0.01 | 0.04 | |
getAnno | 0.09 | 0.03 | 0.12 | |
getCorrelationBlocks | 0.02 | 0.04 | 0.05 | |
getGeno | 0.11 | 0.01 | 0.14 | |
getMethData | 0.12 | 0.02 | 0.14 | |
getOverlapUniverse | 0.10 | 0.03 | 0.12 | |
getOverlappingQTL | 0.01 | 0.00 | 0.02 | |
getPheno | 0.08 | 0.01 | 0.09 | |
getResult | 0.02 | 0.00 | 0.02 | |
getResultGWASMap | 0.04 | 0.05 | 0.09 | |
getSamples | 0.07 | 0.00 | 0.06 | |
getSpecificQTL | 0.02 | 0.00 | 0.02 | |
imputeMeth | 0.17 | 0.11 | 0.32 | |
joinMethQTLResult | 0.04 | 0.00 | 0.05 | |
loadMethQTLInput | 0.07 | 0.02 | 0.07 | |
loadMethQTLResult | 0.01 | 0.00 | 0.02 | |
overlapInputs | 0.05 | 0.01 | 0.08 | |
overlapQTLs | 0.01 | 0.00 | 0.01 | |
qtlAnnotationEnrichment | 0.86 | 0.03 | 0.93 | |
qtlBaseSubstitutionEnrichment | 0.05 | 0.00 | 0.05 | |
qtlDistanceScatterplot | 0.54 | 0.00 | 0.55 | |
qtlGetOption | 0 | 0 | 0 | |
qtlJSON2options | 0 | 0 | 0 | |
qtlManhattanPlot | 0.06 | 0.00 | 0.08 | |
qtlOptions2JSON | 0.00 | 0.00 | 0.01 | |
qtlPlotBaseSubstitution | 0.06 | 0.00 | 0.07 | |
qtlPlotClusterSize | 0.17 | 0.03 | 0.20 | |
qtlPlotSNPCpGInteraction | 0.24 | 0.05 | 0.28 | |
qtlSetOption | 0 | 0 | 0 | |
qtlTFBSMotifEnrichment | 0.01 | 0.00 | 0.01 | |
qtlUpSetPlotCorBlocks | 1.10 | 0.01 | 1.11 | |
qtlUpSetPlotTagCpGs | 0.37 | 0.02 | 0.39 | |
qtlUpsetPlot | 0.36 | 0.01 | 0.38 | |
qtlVennPlot | 0.27 | 0.16 | 0.45 | |
saveMethQTLInput | 0.22 | 0.03 | 0.31 | |
saveMethQTLResult | 0.15 | 0.00 | 0.16 | |