Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:49 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the recoup package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/recoup.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1544/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
recoup 1.20.1 (landing page) Panagiotis Moulos
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: recoup |
Version: 1.20.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:recoup.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings recoup_1.20.1.tar.gz |
StartedAt: 2021-10-14 22:58:47 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 23:07:41 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 533.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: recoup.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:recoup.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings recoup_1.20.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/recoup.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘recoup/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘recoup’ version ‘1.20.1’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘recoup’ 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 R 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 Unexported objects imported by ':::' calls: ‘GenomicFeatures:::GFF_FEATURE_TYPES’ ‘biomaRt:::.generateFilterXML’ ‘biomaRt:::.setResultColNames’ ‘biomaRt:::martCheck’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’ ‘biomaRt:::martVSchema’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE readBamIntervals: no visible binding for global variable ‘bam.file’ recoupCorrelation: no visible binding for global variable ‘Index’ recoupCorrelation: no visible binding for global variable ‘Coverage’ recoupCorrelation: no visible binding for global variable ‘Condition’ recoupCorrelation: no visible binding for global variable ‘Design’ recoupHeatmap : <anonymous>: no visible global function definition for ‘grid.text’ recoupProfile: no visible binding for global variable ‘Signal’ recoupProfile: no visible binding for global variable ‘Condition’ recoupProfile: no visible binding for global variable ‘Design’ Undefined global functions or variables: Condition Coverage Design Index Signal bam.file grid.text * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed mergeRuns 29.399 5.695 26.238 profileMatrix 16.410 4.223 11.505 recoup 12.962 3.048 11.162 recoupPlot 12.914 3.086 10.826 sliceObj 11.148 2.773 9.046 kmeansDesign 11.159 2.500 8.955 simpleGetSet 9.976 2.555 8.126 recoupCorrelation 6.812 0.719 7.317 recoupHeatmap 6.653 0.645 7.150 recoupProfile 6.210 0.747 6.663 coverageRef 5.401 0.102 5.506 buildCustomAnnotation 4.868 0.197 5.099 getAnnotation 4.020 0.051 42.155 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/recoup.Rcheck/00check.log’ for details.
recoup.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL recoup ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘recoup’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (recoup)
recoup.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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("recoup") Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname 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 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 Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Attaching package: 'grid' The following object is masked from 'package:Biostrings': pattern ======================================== ComplexHeatmap version 2.8.0 Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/ Github page: https://github.com/jokergoo/ComplexHeatmap Documentation: http://jokergoo.github.io/ComplexHeatmap-reference If you use it in published research, please cite: Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 2016. The new InteractiveComplexHeatmap package can directly export static complex heatmaps into an interactive Shiny app with zero effort. Have a try! This message can be suppressed by: suppressPackageStartupMessages(library(ComplexHeatmap)) ======================================== Getting main ranges for measurements measurement type: chipseq genomic region type: tss Calculating requested regions coverage for WT H4K20me1 calculating total coverage processing chr12 Calculating requested regions coverage for Set8KO H4K20me1 calculating total coverage processing chr12 Calculating profile for WT H4K20me1 Calculating profile for Set8KO H4K20me1 Constructing genomic coverage profile curve(s) The resolution of the requested profiles will be lowered to avoid increased computation time and/or storage space for heatmap profiles... Calculating tss profile for WT H4K20me1 Calculating tss profile for Set8KO H4K20me1 Constructing genomic coverage heatmap(s) Constructing coverage correlation profile curve(s) dev.new(): using pdf(file="Rplots1.pdf") dev.new(): using pdf(file="Rplots2.pdf") Getting main ranges for measurements measurement type: chipseq genomic region type: genebody Calculating requested regions coverage for WT H4K20me1 calculating total coverage processing chr12 Calculating requested regions coverage for Set8KO H4K20me1 calculating total coverage processing chr12 Calculating profile for WT H4K20me1 center upstream downstream Calculating profile for Set8KO H4K20me1 center upstream downstream Constructing genomic coverage profile curve(s) Using provided design to facet the coverage profiles Constructing genomic coverage heatmap(s) Using provided design to facet the coverage profiles Constructing coverage correlation profile curve(s) Using provided design to facet the coverage profiles dev.new(): using pdf(file="Rplots3.pdf") dev.new(): using pdf(file="Rplots4.pdf") dev.new(): using pdf(file="Rplots5.pdf") RUNIT TEST PROTOCOL -- Thu Oct 14 23:07:31 2021 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : recoup RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 53.695 10.856 49.107
recoup.Rcheck/recoup-Ex.timings
name | user | system | elapsed | |
buildAnnotationDatabase | 0 | 0 | 0 | |
buildAnnotationStore | 0 | 0 | 0 | |
buildCustomAnnotation | 4.868 | 0.197 | 5.099 | |
calcCoverage | 2.629 | 0.068 | 2.700 | |
coverageRef | 5.401 | 0.102 | 5.506 | |
coverageRnaRef | 0 | 0 | 0 | |
getAnnotation | 4.020 | 0.051 | 42.155 | |
getBiotypes | 0.000 | 0.000 | 0.001 | |
getInstalledAnnotations | 0.001 | 0.001 | 0.002 | |
importCustomAnnotation | 1.283 | 0.010 | 1.295 | |
kmeansDesign | 11.159 | 2.500 | 8.955 | |
loadAnnotation | 0.001 | 0.000 | 0.001 | |
mergeRuns | 29.399 | 5.695 | 26.238 | |
preprocessRanges | 0.325 | 0.027 | 0.355 | |
profileMatrix | 16.410 | 4.223 | 11.505 | |
recoup | 12.962 | 3.048 | 11.162 | |
recoupCorrelation | 6.812 | 0.719 | 7.317 | |
recoupHeatmap | 6.653 | 0.645 | 7.150 | |
recoupPlot | 12.914 | 3.086 | 10.826 | |
recoupProfile | 6.210 | 0.747 | 6.663 | |
removeData | 0.023 | 0.006 | 0.029 | |
rpMatrix | 0.939 | 0.088 | 1.026 | |
simpleGetSet | 9.976 | 2.555 | 8.126 | |
sliceObj | 11.148 | 2.773 | 9.046 | |