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 1569/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
plyinteractions 1.4.0 (landing page) Jacques Serizay
| 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 plyinteractions package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/plyinteractions.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: plyinteractions |
Version: 1.4.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:plyinteractions.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings plyinteractions_1.4.0.tar.gz |
StartedAt: 2024-12-20 07:44:41 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 07:54:11 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 569.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: plyinteractions.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:plyinteractions.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings plyinteractions_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/plyinteractions.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 ‘plyinteractions/DESCRIPTION’ ... OK * this is package ‘plyinteractions’ version ‘1.4.0’ * 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 ‘plyinteractions’ 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 ... NOTE count.GInteractions: no visible binding for global variable ‘group’ pair_granges: no visible global function definition for ‘combn’ write_bedpe: no visible binding for global variable ‘name’ write_bedpe: no visible binding for global variable ‘score’ write_pairs: no visible binding for global variable ‘name’ Undefined global functions or variables: combn group name score Consider adding importFrom("utils", "combn") 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed ginteractions-annotate 4.94 0.121 5.077 * 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-3.20-bioc/meat/plyinteractions.Rcheck/00check.log’ for details.
plyinteractions.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL plyinteractions ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘plyinteractions’ ... ** using staged installation ** R ** data ** 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 (plyinteractions)
plyinteractions.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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(plyinteractions) Attaching package: 'plyinteractions' The following object is masked from 'package:stats': filter > > gi <- read.table(text = " + chr1 11 20 chr1 21 30 + + + chr1 11 20 chr1 51 55 + + + chr1 11 30 chr1 51 55 - - + chr1 11 30 chr2 51 60 - -", + col.names = c( + "seqnames1", "start1", "end1", + "seqnames2", "start2", "end2", "strand1", "strand2") + ) |> + as_ginteractions() |> + mutate(score = runif(4), type = c('cis', 'cis', 'cis', 'trans')) > > test_check("plyinteractions") GInteractions object with 4 interactions and 2 metadata columns: seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric> [1] chr1 11-20 + --- chr1 21-30 + | 0.86091538 [2] chr1 11-20 + --- chr1 51-55 + | 0.64031061 [3] chr1 11-30 - --- chr1 51-55 - | 0.00949576 [4] chr1 11-30 - --- chr2 51-60 - | 0.23255051 type <character> [1] cis [2] cis [3] cis [4] trans ------- regions: 6 ranges and 0 metadata columns seqinfo: 2 sequences from an unspecified genome; no seqlengths PinnedGInteractions object with 4 interactions and 2 metadata columns: Pinned on: anchors2 seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric> [1] chr1 11-20 + --- chr1 21-30 + | 0.86091538 [2] chr1 11-20 + --- chr1 51-55 + | 0.64031061 [3] chr1 11-30 - --- chr1 51-55 - | 0.00949576 [4] chr1 11-30 - --- chr2 51-60 - | 0.23255051 type <character> [1] cis [2] cis [3] cis [4] trans ------- regions: 6 ranges and 0 metadata columns seqinfo: 2 sequences from an unspecified genome; no seqlengths AnchoredPinnedGInteractions object with 4 interactions and 2 metadata columns: Pinned on: anchors2 | Anchored by: 5p seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric> [1] chr1 11-20 + --- chr1 21-30 + | 0.86091538 [2] chr1 11-20 + --- chr1 51-55 + | 0.64031061 [3] chr1 11-30 - --- chr1 51-55 - | 0.00949576 [4] chr1 11-30 - --- chr2 51-60 - | 0.23255051 type <character> [1] cis [2] cis [3] cis [4] trans ------- regions: 6 ranges and 0 metadata columns seqinfo: 2 sequences from an unspecified genome; no seqlengths GroupedGInteractions object with 4 interactions and 3 metadata columns: Groups: group [2] seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric> [1] chr1 11-20 + --- chr1 21-30 + | 0.86091538 [2] chr1 11-20 + --- chr1 51-55 + | 0.64031061 [3] chr1 11-30 - --- chr1 51-55 - | 0.00949576 [4] chr1 11-30 - --- chr2 51-60 - | 0.23255051 type group <character> <numeric> [1] cis 1 [2] cis 1 [3] cis 2 [4] trans 2 ------- regions: 6 ranges and 0 metadata columns seqinfo: 2 sequences from an unspecified genome; no seqlengths AnchoredPinnedGInteractions object with 4 interactions and 2 metadata columns: Pinned on: anchors2 | Anchored by: 5p seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score <Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric> [1] chr1 11-20 + --- chr1 21-30 + | 0.86091538 [2] chr1 11-20 + --- chr1 51-55 + | 0.64031061 [3] chr1 11-30 - --- chr1 51-55 - | 0.00949576 [4] chr1 11-30 - --- chr2 51-60 - | 0.23255051 type <character> [1] cis [2] cis [3] cis [4] trans ------- regions: 6 ranges and 0 metadata columns seqinfo: 2 sequences from an unspecified genome; no seqlengths Detected `seqlengths:` chr1 chr2 55 60 Provided `seqlengths:` chr1 chr2 100 30 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 188 ] > > proc.time() user system elapsed 45.129 1.763 47.747
plyinteractions.Rcheck/plyinteractions-Ex.timings
name | user | system | elapsed | |
add-pairdist | 0.447 | 0.009 | 0.456 | |
dplyr-arrange | 1.527 | 0.196 | 1.727 | |
dplyr-count | 1.824 | 0.042 | 1.869 | |
dplyr-filter | 1.277 | 0.015 | 1.295 | |
dplyr-group_by | 1.692 | 0.014 | 1.709 | |
dplyr-mutate | 3.370 | 0.017 | 3.394 | |
dplyr-rename | 0.364 | 0.003 | 0.369 | |
dplyr-select | 0.711 | 0.011 | 0.725 | |
dplyr-slice | 0.215 | 0.005 | 0.220 | |
dplyr-summarize | 1.434 | 0.008 | 1.445 | |
ginteractions-anchor | 0.395 | 0.003 | 0.398 | |
ginteractions-annotate | 4.940 | 0.121 | 5.077 | |
ginteractions-construct | 1.490 | 0.053 | 1.548 | |
ginteractions-count-overlaps | 0.871 | 0.006 | 0.878 | |
ginteractions-export | 0.247 | 0.002 | 0.250 | |
ginteractions-filter-overlaps | 1.076 | 0.025 | 1.103 | |
ginteractions-find-overlaps | 1.169 | 0.014 | 1.185 | |
ginteractions-getters | 0.420 | 0.007 | 0.447 | |
ginteractions-join-overlap-left | 1.764 | 0.025 | 1.871 | |
ginteractions-pin | 0.626 | 0.012 | 0.670 | |
group-group_data | 0.491 | 0.006 | 0.523 | |
pair-granges | 0.081 | 0.003 | 0.089 | |
plyranges-flank | 1.095 | 0.009 | 1.157 | |
plyranges-shift | 1.385 | 0.023 | 1.479 | |
plyranges-stretch | 1.478 | 0.037 | 1.571 | |
reexports | 0.000 | 0.001 | 0.001 | |
replace_anchors | 1.617 | 0.017 | 1.713 | |