Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:42 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the MetCirc package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1096/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MetCirc 1.22.0 (landing page) Thomas Naake
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: MetCirc |
Version: 1.22.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MetCirc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MetCirc_1.22.0.tar.gz |
StartedAt: 2021-10-14 20:54:21 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:59:55 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 334.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MetCirc.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MetCirc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MetCirc_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/MetCirc.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MetCirc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MetCirc’ version ‘1.22.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt 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 ‘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 R 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: ‘MSnbase:::bin_Spectra’ ‘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’ ‘spectraCond’ ‘typeMatch_link0’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE plotSpectra: no visible binding for global variable ‘mz’ plotSpectra: no visible binding for global variable ‘int’ Undefined global functions or variables: int mz * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed createLinkDf 6.977 0.123 7.104 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/MetCirc.Rcheck/00check.log’ for details.
MetCirc.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MetCirc ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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 0.4.13 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: MSnbase Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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, 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: mzR Loading required package: Rcpp Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth This is MSnbase version 2.18.0 Visit https://lgatto.github.io/MSnbase/ to get started. Attaching package: 'MSnbase' The following object is masked from 'package:base': trimws > > test_check("MetCirc") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 181 ] > > proc.time() user system elapsed 122.409 1.240 123.816
MetCirc.Rcheck/MetCirc-Ex.timings
name | user | system | elapsed | |
cart2Polar | 0.001 | 0.001 | 0.001 | |
circosLegend | 1.323 | 0.112 | 1.436 | |
compare_Spectra | 0.288 | 0.007 | 0.295 | |
convertMsp2Spectra | 0.344 | 0.018 | 0.362 | |
createLink0df | 3.468 | 0.086 | 3.561 | |
createLinkDf | 6.977 | 0.123 | 7.104 | |
cutLinkDf | 3.248 | 0.057 | 3.306 | |
getLinkDfIndices | 0.000 | 0.000 | 0.001 | |
highlight | 1.782 | 0.169 | 1.951 | |
minFragCart2Polar | 0.978 | 0.183 | 1.163 | |
neutralloss | 0.025 | 0.001 | 0.026 | |
normalizeddotproduct | 0.024 | 0.001 | 0.025 | |
orderSimilarityMatrix | 0.742 | 0.126 | 0.869 | |
plotCircos | 0.840 | 0.033 | 0.873 | |
plotSpectra | 0.377 | 0.019 | 0.397 | |
printInformationSelect | 1.107 | 0.155 | 1.263 | |
recordPlotFill_degreeFeatures | 0.188 | 0.003 | 0.192 | |
recordPlotHighlight | 0.146 | 0.012 | 0.158 | |
replayPlotAdd | 1.441 | 0.126 | 1.569 | |
replayPlotOrder | 0.232 | 0.010 | 0.243 | |
select | 0.000 | 0.000 | 0.001 | |
shinyCircos | 0.701 | 0.088 | 0.790 | |
spectraCond | 0.017 | 0.008 | 0.025 | |
thresholdLinkDf | 3.172 | 0.114 | 3.291 | |
typeMatch_link0 | 0.801 | 0.134 | 0.936 | |