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 12:07 -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 1216/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MetCirc 1.36.0 (landing page) Thomas Naake
| 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 MetCirc package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MetCirc.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: MetCirc |
Version: 1.36.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetCirc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetCirc_1.36.0.tar.gz |
StartedAt: 2024-12-21 00:39:49 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 00:43:14 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 205.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MetCirc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetCirc.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetCirc_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MetCirc.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MetCirc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MetCirc’ version ‘1.36.0’ * 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 ‘MetCirc’ 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 ... NOTE Unexported objects imported by ':::' calls: ‘MsCoreUtils:::.weightxy’ ‘circlize:::get.sector.data’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘recordPlotFill_degreeFeatures’ ‘recordPlotHighlight’ ‘replayPlotAdd’ ‘replayPlotOrder’ ‘select’ ‘spectraCondition’ ‘typeMatch_link0’ * 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) convertExampleDF.Rd:21: Escaped LaTeX specials: \_ checkRd: (-1) convertExampleDF.Rd:22: Escaped LaTeX specials: \_ * 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MetCirc.Rcheck/00check.log’ for details.
MetCirc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MetCirc ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘MetCirc’ ... ** 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 (MetCirc)
MetCirc.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: aarch64-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("MetCirc") Loading required package: amap Loading required package: circlize ======================================== circlize version 0.4.16 CRAN page: https://cran.r-project.org/package=circlize Github page: https://github.com/jokergoo/circlize Documentation: https://jokergoo.github.io/circlize_book/book/ If you use it in published research, please cite: Gu, Z. circlize implements and enhances circular visualization in R. Bioinformatics 2014. This message can be suppressed by: suppressPackageStartupMessages(library(circlize)) ======================================== Loading required package: scales Loading required package: shiny Loading required package: Spectra Loading required package: S4Vectors 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 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: BiocParallel Attaching package: 'MetCirc' The following object is masked from 'package:Spectra': plotSpectra > library("MsCoreUtils") Attaching package: 'MsCoreUtils' The following objects are masked from 'package:Spectra': bin, entropy, smooth The following object is masked from 'package:stats': smooth > > test_check("MetCirc") [ FAIL 0 | WARN 2 | SKIP 0 | PASS 181 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 181 ] > > proc.time() user system elapsed 82.065 1.097 84.423
MetCirc.Rcheck/MetCirc-Ex.timings
name | user | system | elapsed | |
cart2Polar | 0.001 | 0.000 | 0.000 | |
circosLegend | 0.318 | 0.007 | 0.324 | |
convertMsp2Spectra | 0.475 | 0.003 | 0.478 | |
createLink0df | 1.505 | 0.014 | 1.519 | |
createLinkDf | 3.161 | 0.096 | 3.426 | |
cutLinkDf | 1.655 | 0.046 | 1.900 | |
getLinkDfIndices | 0 | 0 | 0 | |
highlight | 0.983 | 0.017 | 1.122 | |
minFragCart2Polar | 0.305 | 0.006 | 0.346 | |
neutralloss | 0.246 | 0.003 | 0.274 | |
orderSimilarityMatrix | 0.247 | 0.004 | 0.279 | |
plotCircos | 0.495 | 0.008 | 0.564 | |
plotSpectra | 0.310 | 0.010 | 0.352 | |
printInformationSelect | 0.283 | 0.003 | 0.301 | |
recordPlotFill_degreeFeatures | 0.101 | 0.004 | 0.108 | |
recordPlotHighlight | 0.151 | 0.005 | 0.158 | |
replayPlotAdd | 0.821 | 0.017 | 0.848 | |
replayPlotOrder | 0.177 | 0.005 | 0.182 | |
select | 0.001 | 0.000 | 0.000 | |
shinyCircos | 0.237 | 0.002 | 0.241 | |
spectraCondition | 0.027 | 0.003 | 0.030 | |
thresholdLinkDf | 1.568 | 0.080 | 1.663 | |
typeMatch_link0 | 0.252 | 0.006 | 0.259 | |