Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-09 17:42 -0400 (Tue, 09 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4709 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 1359/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MsQuality 1.4.0 (landing page) Thomas Naake
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | 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 | OK | OK | |||||||||
To the developers/maintainers of the MsQuality package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsQuality.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: MsQuality |
Version: 1.4.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsQuality.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsQuality_1.4.0.tar.gz |
StartedAt: 2024-07-08 08:19:31 -0400 (Mon, 08 Jul 2024) |
EndedAt: 2024-07-08 08:33:19 -0400 (Mon, 08 Jul 2024) |
EllapsedTime: 827.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MsQuality.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsQuality.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsQuality_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MsQuality.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘MsQuality/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MsQuality’ 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 ‘MsQuality’ 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 ... 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 calculateMetrics 9.826 1.799 10.279 plotMetric 4.765 1.560 10.885 calculateMetricsFromMsExperiment 4.700 1.611 6.610 plotMetricTibble 4.333 1.647 3.951 ticQuartersRtFraction 3.665 1.445 0.367 calculateMetricsFromSpectra 3.876 1.195 5.337 * 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: OK
MsQuality.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsQuality ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘MsQuality’ ... ** 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 (MsQuality)
MsQuality.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: 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("MsQuality") > library("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, 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 Loading required package: ProtGenerics Attaching package: 'ProtGenerics' The following object is masked from 'package:stats': smooth > library("MsExperiment") > library("msdata") > library("S4Vectors") > > test_check("MsQuality") trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest' Content type 'application/json; charset=utf-8' length 7201 bytes ================================================== downloaded 7201 bytes trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.157/psi-ms.obo' Content type 'application/octet-stream' length 985525 bytes (962 KB) ================================================== downloaded 962 KB [ FAIL 0 | WARN 0 | SKIP 0 | PASS 866 ] > > proc.time() user system elapsed 189.321 45.680 195.605
MsQuality.Rcheck/MsQuality-Ex.timings
name | user | system | elapsed | |
MsQuality-package | 0.000 | 0.001 | 0.001 | |
areaUnderTic | 0.375 | 0.031 | 0.450 | |
areaUnderTicRtQuantiles | 0.415 | 0.011 | 0.475 | |
calculateMetrics | 9.826 | 1.799 | 10.279 | |
calculateMetricsFromMsExperiment | 4.700 | 1.611 | 6.610 | |
calculateMetricsFromOneSampleSpectra | 3.491 | 0.586 | 4.461 | |
calculateMetricsFromSpectra | 3.876 | 1.195 | 5.337 | |
chromatographyDuration | 3.346 | 0.922 | 0.334 | |
dot-rtOrderSpectra | 0.251 | 0.037 | 0.310 | |
extentIdentifiedPrecursorIntensity | 0.224 | 0.027 | 0.280 | |
meanCharge | 0.217 | 0.025 | 0.273 | |
medianCharge | 0.214 | 0.024 | 0.266 | |
medianPrecursorMz | 0.214 | 0.024 | 0.269 | |
medianTicOfRtRange | 0.215 | 0.023 | 0.257 | |
medianTicRtIqr | 0.222 | 0.026 | 0.273 | |
msSignal10xChange | 0.225 | 0.025 | 0.271 | |
mzAcquisitionRange | 0.214 | 0.025 | 0.276 | |
numberEmptyScans | 0.239 | 0.023 | 0.306 | |
numberSpectra | 0.206 | 0.020 | 0.249 | |
plotMetric | 4.765 | 1.560 | 10.885 | |
plotMetricTibble | 4.333 | 1.647 | 3.951 | |
precursorIntensityMean | 0.236 | 0.035 | 0.303 | |
precursorIntensityQuartiles | 0.236 | 0.026 | 0.311 | |
precursorIntensityRange | 0.224 | 0.025 | 0.286 | |
precursorIntensitySd | 0.229 | 0.025 | 0.290 | |
qualityMetrics | 0.223 | 0.027 | 0.283 | |
ratioCharge1over2 | 0.221 | 0.026 | 0.287 | |
ratioCharge3over2 | 0.220 | 0.023 | 0.279 | |
ratioCharge4over2 | 0.216 | 0.022 | 0.273 | |
rtAcquisitionRange | 0.219 | 0.021 | 0.280 | |
rtIqr | 0.228 | 0.023 | 0.294 | |
rtIqrRate | 0.220 | 0.022 | 0.293 | |
rtOverMsQuarters | 0.219 | 0.024 | 0.291 | |
shinyMsQuality | 0.911 | 0.351 | 3.900 | |
ticQuartersRtFraction | 3.665 | 1.445 | 0.367 | |
ticQuartileToQuartileLogRatio | 0.226 | 0.034 | 0.292 | |
transformIntoMzQC | 0.922 | 0.804 | 1.267 | |