Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 826/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicInteractions 1.40.0 (landing page) Liz Ing-Simmons
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the GenomicInteractions package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicInteractions.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: GenomicInteractions |
Version: 1.40.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicInteractions.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicInteractions_1.40.0.tar.gz |
StartedAt: 2024-12-20 03:53:02 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 04:05:07 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 725.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicInteractions.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomicInteractions.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomicInteractions_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenomicInteractions.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicInteractions/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GenomicInteractions’ version ‘1.40.0’ * 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 ‘GenomicInteractions’ can be installed ... OK * checking installed package size ... NOTE installed size is 9.2Mb sub-directories of 1Mb or more: extdata 7.9Mb * 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: BUG FIXES * 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 plotCisTrans: no visible global function definition for 'head' plotInteractionAnnotations: no visible global function definition for 'head' Undefined global functions or variables: head Consider adding importFrom("utils", "head") to your NAMESPACE file. * 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 data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/GenomicInteractions.Rcheck/00check.log’ for details.
GenomicInteractions.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomicInteractions ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘GenomicInteractions’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomicInteractions)
GenomicInteractions.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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(GenomicInteractions) 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': 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, saveRDS, 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': 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("GenomicInteractions") [ FAIL 0 | WARN 3 | SKIP 0 | PASS 57 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 57 ] > > proc.time() user system elapsed 46.036 2.235 50.445
GenomicInteractions.Rcheck/GenomicInteractions-Ex.timings
name | user | system | elapsed | |
GInteractions-subsetByFeatures-methods | 0.277 | 0.012 | 0.293 | |
GenomicInteractions-class | 0.252 | 0.004 | 0.269 | |
GenomicInteractions | 0.186 | 0.003 | 0.197 | |
InteractionHelpers | 0.081 | 0.007 | 0.087 | |
InteractionTrack | 1.648 | 0.188 | 2.149 | |
annotateInteractions | 0.587 | 0.031 | 0.647 | |
annotateRegions | 0.095 | 0.005 | 0.104 | |
asBED-GInteractions-method | 0.582 | 0.009 | 0.593 | |
availableDisplayPars | 0.039 | 0.006 | 0.044 | |
calculateDistances | 0.130 | 0.001 | 0.132 | |
categoriseInteractions | 0.455 | 0.011 | 0.481 | |
export.bed12 | 2.238 | 0.024 | 2.305 | |
export.bedpe | 0.232 | 0.012 | 0.244 | |
export.chiasig | 0.157 | 0.010 | 0.168 | |
export.igraph | 0.158 | 0.017 | 0.176 | |
getters | 0.158 | 0.002 | 0.161 | |
makeGenomicInteractionsFromFile | 1.182 | 0.056 | 1.254 | |
plotAvgViewpoint | 0.492 | 0.008 | 0.501 | |
plotCisTrans | 0.552 | 0.024 | 0.579 | |
plotCounts | 0.602 | 0.009 | 0.615 | |
plotDists | 0.347 | 0.009 | 0.362 | |
plotInteractionAnnotations | 0.743 | 0.012 | 0.758 | |
plotSummaryStats | 1.599 | 0.135 | 1.745 | |
plotViewpoint | 0.796 | 0.007 | 0.813 | |
resetAnnotations | 0.055 | 0.004 | 0.060 | |
setters | 0.171 | 0.001 | 0.173 | |
summariseByFeaturePairs | 1.826 | 0.024 | 1.867 | |
summariseByFeatures | 0.937 | 0.058 | 1.013 | |
viewPoint | 0.433 | 0.006 | 0.444 | |