Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:47 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 1550/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
plyranges 1.25.0 (landing page) Michael Love
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the plyranges package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/plyranges.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: plyranges |
Version: 1.25.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:plyranges.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings plyranges_1.25.0.tar.gz |
StartedAt: 2024-08-27 07:49:24 -0000 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 07:55:20 -0000 (Tue, 27 Aug 2024) |
EllapsedTime: 356.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: plyranges.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:plyranges.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings plyranges_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/plyranges.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘plyranges/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘plyranges’ version ‘1.25.0’ * 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 ‘plyranges’ 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) group_by-ranges.Rd:57: Lost braces in \itemize; meant \describe ? checkRd: (-1) group_by-ranges.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) ranges-anchor.Rd:58: Lost braces in \itemize; meant \describe ? checkRd: (-1) ranges-anchor.Rd:59: Lost braces in \itemize; meant \describe ? checkRd: (-1) ranges-anchor.Rd:60: Lost braces in \itemize; meant \describe ? checkRd: (-1) ranges-anchor.Rd:61-62: Lost braces in \itemize; meant \describe ? checkRd: (-1) ranges-anchor.Rd:63-64: Lost braces in \itemize; meant \describe ? * 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 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/plyranges.Rcheck/00check.log’ for details.
plyranges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL plyranges ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘plyranges’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (plyranges)
plyranges.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" 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. > library(testthat) > library(plyranges) 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: IRanges Loading required package: S4Vectors Loading required package: stats4 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: GenomicRanges Loading required package: GenomeInfoDb Attaching package: 'plyranges' The following object is masked from 'package:IRanges': slice The following object is masked from 'package:stats': filter > > test_check("plyranges") [ FAIL 0 | WARN 8 | SKIP 0 | PASS 395 ] [ FAIL 0 | WARN 8 | SKIP 0 | PASS 395 ] > > proc.time() user system elapsed 58.008 2.274 60.388
plyranges.Rcheck/plyranges-Ex.timings
name | user | system | elapsed | |
add-nearest-distance | 0.463 | 0.000 | 0.464 | |
as_ranges | 0.120 | 0.000 | 0.121 | |
compute_coverage | 0.021 | 0.001 | 0.022 | |
element-setops | 0.134 | 0.007 | 0.144 | |
filter-ranges | 0.689 | 0.083 | 0.774 | |
group_by-ranges | 0.371 | 0.016 | 0.387 | |
io-bam-read | 0.766 | 0.032 | 0.800 | |
io-bed-read | 1.438 | 0.056 | 1.497 | |
io-bed-write | 0 | 0 | 0 | |
io-bigwig-read | 0.14 | 0.00 | 0.14 | |
io-bigwig-write | 0 | 0 | 0 | |
io-gff-read | 0.477 | 0.016 | 0.494 | |
io-gff-write | 0.000 | 0.000 | 0.001 | |
io-wig-read | 0.459 | 0.032 | 0.494 | |
mutate-ranges | 1.963 | 0.096 | 2.062 | |
n | 0.308 | 0.012 | 0.321 | |
n_distinct | 0.039 | 0.000 | 0.040 | |
overlap-joins | 0.240 | 0.008 | 0.248 | |
ranges-anchor | 0.134 | 0.000 | 0.133 | |
ranges-arrange | 0.064 | 0.000 | 0.063 | |
ranges-bind | 0.243 | 0.004 | 0.247 | |
ranges-chop | 0.439 | 0.008 | 0.447 | |
ranges-construct | 0.132 | 0.000 | 0.132 | |
ranges-count-overlaps | 0.076 | 0.000 | 0.077 | |
ranges-disjoin | 0.928 | 0.015 | 0.944 | |
ranges-expand | 0.699 | 0.013 | 0.713 | |
ranges-filter-overlaps | 0.175 | 0.000 | 0.175 | |
ranges-flank | 0.126 | 0.004 | 0.130 | |
ranges-follow | 0.210 | 0.000 | 0.211 | |
ranges-info | 0.063 | 0.000 | 0.064 | |
ranges-interweave | 0.190 | 0.003 | 0.194 | |
ranges-names | 0.172 | 0.008 | 0.180 | |
ranges-nearest | 0.526 | 0.016 | 0.543 | |
ranges-overlaps-self | 0.167 | 0.004 | 0.172 | |
ranges-overlaps | 0.242 | 0.012 | 0.254 | |
ranges-pairs | 0.449 | 0.004 | 0.454 | |
ranges-precede | 0.197 | 0.000 | 0.197 | |
ranges-reduce | 1.223 | 0.024 | 1.249 | |
ranges-select | 0.102 | 0.004 | 0.106 | |
ranges-setops | 1.115 | 0.028 | 1.146 | |
ranges-shift | 0.192 | 0.000 | 0.193 | |
ranges-summarise | 0.176 | 0.008 | 0.184 | |
ranges-tile | 0.120 | 0.000 | 0.121 | |
slice-ranges | 0.767 | 0.008 | 0.776 | |
stretch | 0.279 | 0.000 | 0.280 | |