Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-25 17:42 -0400 (Tue, 25 Jun 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" | 4760 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 1585/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
plyranges 1.24.0 (landing page) Michael Love
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | 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. |
Package: plyranges |
Version: 1.24.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:plyranges.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings plyranges_1.24.0.tar.gz |
StartedAt: 2024-06-24 09:32:07 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 09:43:59 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 711.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: plyranges.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:plyranges.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings plyranges_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/plyranges.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘plyranges/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘plyranges’ version ‘1.24.0’ * 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 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed io-bed-read 6.026 1.197 8.297 * 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 ‘/Users/biocbuild/bbs-3.19-bioc/meat/plyranges.Rcheck/00check.log’ for details.
plyranges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL plyranges ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.0 (2024-04-24) -- "Puppy Cup" 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(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 103.958 3.646 120.738
plyranges.Rcheck/plyranges-Ex.timings
name | user | system | elapsed | |
add-nearest-distance | 0.842 | 0.074 | 1.059 | |
as_ranges | 0.219 | 0.030 | 0.293 | |
compute_coverage | 0.039 | 0.007 | 0.051 | |
element-setops | 0.275 | 0.043 | 0.374 | |
filter-ranges | 1.379 | 0.048 | 1.650 | |
group_by-ranges | 0.731 | 0.009 | 0.858 | |
io-bam-read | 1.134 | 0.054 | 1.379 | |
io-bed-read | 6.026 | 1.197 | 8.297 | |
io-bed-write | 0.001 | 0.001 | 0.002 | |
io-bigwig-read | 0.244 | 0.018 | 0.321 | |
io-bigwig-write | 0.001 | 0.000 | 0.001 | |
io-gff-read | 0.940 | 0.111 | 1.170 | |
io-gff-write | 0.000 | 0.001 | 0.000 | |
io-wig-read | 0.801 | 0.100 | 1.114 | |
mutate-ranges | 1.845 | 0.095 | 2.234 | |
n | 0.615 | 0.004 | 0.702 | |
n_distinct | 0.075 | 0.001 | 0.087 | |
overlap-joins | 0.469 | 0.006 | 0.542 | |
ranges-anchor | 0.260 | 0.005 | 0.313 | |
ranges-arrange | 0.114 | 0.003 | 0.134 | |
ranges-bind | 0.425 | 0.021 | 0.516 | |
ranges-chop | 0.712 | 0.014 | 0.838 | |
ranges-construct | 0.242 | 0.007 | 0.280 | |
ranges-count-overlaps | 0.143 | 0.002 | 0.169 | |
ranges-disjoin | 1.660 | 0.014 | 1.862 | |
ranges-expand | 1.151 | 0.015 | 1.302 | |
ranges-filter-overlaps | 0.316 | 0.005 | 0.356 | |
ranges-flank | 0.243 | 0.004 | 0.273 | |
ranges-follow | 0.387 | 0.005 | 0.438 | |
ranges-info | 0.117 | 0.004 | 0.144 | |
ranges-interweave | 0.351 | 0.007 | 0.417 | |
ranges-names | 0.284 | 0.005 | 0.324 | |
ranges-nearest | 1.020 | 0.013 | 1.160 | |
ranges-overlaps-self | 0.302 | 0.006 | 0.345 | |
ranges-overlaps | 0.411 | 0.012 | 0.473 | |
ranges-pairs | 0.820 | 0.013 | 0.946 | |
ranges-precede | 0.390 | 0.008 | 0.456 | |
ranges-reduce | 2.311 | 0.019 | 2.691 | |
ranges-select | 0.173 | 0.010 | 0.211 | |
ranges-setops | 1.953 | 0.014 | 2.289 | |
ranges-shift | 0.348 | 0.007 | 0.410 | |
ranges-summarise | 0.339 | 0.003 | 0.398 | |
ranges-tile | 0.218 | 0.006 | 0.264 | |
slice-ranges | 1.374 | 0.014 | 1.630 | |
stretch | 0.537 | 0.006 | 0.620 | |