Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-01-25 15:39 -0500 (Sat, 25 Jan 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4658 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4455 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4408 |
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 1702/2286 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
recoup 1.35.0 (landing page) Panagiotis Moulos
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the recoup package: - 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 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: recoup |
Version: 1.35.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:recoup.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings recoup_1.35.0.tar.gz |
StartedAt: 2025-01-25 10:44:30 -0000 (Sat, 25 Jan 2025) |
EndedAt: 2025-01-25 10:53:40 -0000 (Sat, 25 Jan 2025) |
EllapsedTime: 550.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: recoup.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:recoup.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings recoup_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/recoup.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘recoup/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘recoup’ version ‘1.35.0’ * 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 ‘recoup’ can be installed ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/recoup.Rcheck/00install.out’ for details. * 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 Unexported objects imported by ':::' calls: ‘biomaRt:::.generateFilterXML’ ‘biomaRt:::.setResultColNames’ ‘biomaRt:::martCheck’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’ ‘biomaRt:::martVSchema’ ‘txdbmaker:::GFF_FEATURE_TYPES’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘makeHorizontalAnnotation’ * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 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 ... NOTE checkRd: (-1) recoup.Rd:210-211: Lost braces 210 | \code{region}{Minimum flank is 0bp and maximum is | ^ * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: coverageRef.Rd: makeGRangesFromDataFrame recoup.Rd: GRanges, findOverlaps, ggplot, Heatmap, makeGRangesFromDataFrame recoupPlot.Rd: draw rpMatrix.Rd: makeGRangesFromDataFrame Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 28.467 9.392 29.436 profileMatrix 13.893 4.686 10.248 recoup 11.356 4.691 11.150 recoupPlot 11.190 4.663 11.488 sliceObj 10.579 4.500 10.462 simpleGetSet 10.132 4.142 10.051 kmeansDesign 10.597 3.556 10.203 recoupProfile 7.487 2.471 9.222 recoupCorrelation 7.481 2.128 8.829 recoupHeatmap 7.379 2.167 8.806 coverageRef 6.456 0.148 6.613 getAnnotation 1.980 0.099 6.445 * 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: 5 WARNINGs, 7 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/recoup.Rcheck/00check.log’ for details.
recoup.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL recoup ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘recoup’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (recoup)
recoup.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > BiocGenerics:::testPackage("recoup") 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 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches 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 2.23.0 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 either one: - Gu, Z. Complex Heatmap Visualization. iMeta 2022. - 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)) ======================================== Warning: program compiled against libxml 212 using older 211 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 -- Sat Jan 25 10:53:35 2025 *********************************************** 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 50.634 11.958 48.549
recoup.Rcheck/recoup-Ex.timings
name | user | system | elapsed | |
buildAnnotationDatabase | 0 | 0 | 0 | |
buildAnnotationStore | 0 | 0 | 0 | |
buildCustomAnnotation | 3.260 | 0.064 | 3.334 | |
calcCoverage | 4.145 | 0.018 | 4.170 | |
coverageRef | 6.456 | 0.148 | 6.613 | |
coverageRnaRef | 0 | 0 | 0 | |
getAnnotation | 1.980 | 0.099 | 6.445 | |
getBiotypes | 0.000 | 0.000 | 0.001 | |
getInstalledAnnotations | 0.001 | 0.000 | 0.001 | |
importCustomAnnotation | 1.118 | 0.075 | 1.201 | |
kmeansDesign | 10.597 | 3.556 | 10.203 | |
loadAnnotation | 0.001 | 0.000 | 0.001 | |
mergeRuns | 28.467 | 9.392 | 29.436 | |
preprocessRanges | 0.270 | 0.088 | 0.363 | |
profileMatrix | 13.893 | 4.686 | 10.248 | |
recoup | 11.356 | 4.691 | 11.150 | |
recoupCorrelation | 7.481 | 2.128 | 8.829 | |
recoupHeatmap | 7.379 | 2.167 | 8.806 | |
recoupPlot | 11.190 | 4.663 | 11.488 | |
recoupProfile | 7.487 | 2.471 | 9.222 | |
removeData | 0.108 | 0.097 | 0.026 | |
rpMatrix | 0.877 | 0.127 | 1.007 | |
simpleGetSet | 10.132 | 4.142 | 10.051 | |
sliceObj | 10.579 | 4.500 | 10.462 | |