Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-31 17:02:51 -0400 (Fri, 31 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4753 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
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 242/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BRGenomics 1.16.0 (landing page) Mike DeBerardine
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | TIMEOUT | OK | |||||||||
To the developers/maintainers of the BRGenomics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BRGenomics.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: BRGenomics |
Version: 1.16.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BRGenomics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BRGenomics_1.16.0.tar.gz |
StartedAt: 2024-05-31 01:50:29 -0400 (Fri, 31 May 2024) |
EndedAt: 2024-05-31 02:30:29 -0400 (Fri, 31 May 2024) |
EllapsedTime: 2400.2 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: BRGenomics.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BRGenomics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BRGenomics_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/BRGenomics.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘BRGenomics/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BRGenomics’ version ‘1.16.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘BRGenomics’ 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 loading without being on the library search path ... 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 ... OK * checking Rd files ... NOTE checkRd: (-1) binNdimensions.Rd:95: Lost braces 95 | code{use_bin_numbers = FALSE}, the center points of the bins are returned | ^ checkRd: (-1) mergeGRangesData.Rd:38: Lost braces 38 | makeGRangesBRG}}. This is always set to code{FALSE} if | ^ * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed getDESeqResults 9.434 0.403 9.838 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’
BRGenomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BRGenomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘BRGenomics’ ... ** 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 (BRGenomics)
BRGenomics.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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. > Sys.setenv("R_TESTS" = "") > library(testthat) > library(BRGenomics) Loading required package: rtracklayer 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, 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 > > test_check("BRGenomics")
BRGenomics.Rcheck/BRGenomics-Ex.timings
name | user | system | elapsed | |
applyNFsGRanges | 0.222 | 0.004 | 0.226 | |
binNdimensions | 0.487 | 0.004 | 0.490 | |
bootstrap-signal-by-position | 1.214 | 0.240 | 1.455 | |
genebodies | 0.143 | 0.068 | 0.211 | |
getCountsByPositions | 0.372 | 0.116 | 0.488 | |
getCountsByRegions | 0.161 | 0.112 | 0.274 | |
getDESeqDataSet | 0.55 | 0.10 | 0.65 | |
getDESeqResults | 9.434 | 0.403 | 9.838 | |
getMaxPositionsBySignal | 0.227 | 0.012 | 0.239 | |
getPausingIndices | 0.573 | 0.044 | 0.617 | |
getSpikeInCounts | 0.249 | 0.191 | 0.322 | |
getSpikeInNFs | 0.481 | 0.175 | 0.501 | |
getStrandedCoverage | 0.829 | 0.124 | 0.953 | |
import-functions | 0.765 | 0.123 | 0.890 | |
import_bam | 0.532 | 0.060 | 0.592 | |
intersectByGene | 0.819 | 0.060 | 0.879 | |
makeGRangesBRG | 0.279 | 0.004 | 0.283 | |
mergeGRangesData | 0.899 | 0.048 | 0.947 | |
mergeReplicates | 0.537 | 0.064 | 0.601 | |
subsampleBySpikeIn | 0.629 | 0.266 | 0.725 | |
subsampleGRanges | 0.066 | 0.008 | 0.075 | |
subsetRegionsBySignal | 1.468 | 0.324 | 1.791 | |
tidyChromosomes | 0.572 | 0.032 | 0.603 | |