Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4372 |
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 1203/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
metaMS 1.43.0 (landing page) Yann Guitton
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the metaMS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metaMS.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: metaMS |
Version: 1.43.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:metaMS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings metaMS_1.43.0.tar.gz |
StartedAt: 2024-12-23 09:23:13 -0000 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 09:30:54 -0000 (Mon, 23 Dec 2024) |
EllapsedTime: 461.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: metaMS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:metaMS.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings metaMS_1.43.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/metaMS.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘metaMS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘metaMS’ version ‘1.43.0’ * 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 ‘metaMS’ 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 loading without being on the library search path ... 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: FEMsettings.Rd: findPeaks, annotate metaMSsettings-class.Rd: findPeaks processStandards.Rd: xcmsSet runCAMERA.Rd: annotate, groupFWHM Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 ‘runTests.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 ‘/home/biocbuild/bbs-3.21-bioc/meat/metaMS.Rcheck/00check.log’ for details.
metaMS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL metaMS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘metaMS’ ... ** 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 (metaMS)
metaMS.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu 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. > BiocGenerics:::testPackage("metaMS") Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. This is xcms version 4.5.2 Attaching package: 'xcms' The following object is masked from 'package:stats': sigma < -------- Experiment of 4 samples ------------------------------------- > < -------- Instrument: TSQXLS.QQQ.GC ----------------------------------- > < -------- Annotation using database of 3 spectra ---------------------- > < -------- Using xcmsSet object - only doing annotation ---------------- > < -------- Removing artefacts (Bleeding, Plasticizers) ----------------- > < -------- Matching with database of standards ------------------------- > < -------- Matching unknowns across samples ---------------------------- > < -------- Formatting results ------------------------------------------ > < -------- Done! ------------------------------------------------------- > < -------- Experiment of 4 samples ------------------------------------- > < -------- Instrument: Synapt.QTOF.RP - polarity: positive ------------ > < -------- Database of 4 compounds ------------------------------------- > < -------- Using xcmsSet object - only doing annotation ---------------- > < -------- Performing annotation --------------------------------------- > Fixed mass tolerance 0.005 Feature-wise Annotation ... < -------- Formatting the output --------------------------------------- > < -------- Done ! ------------------------------------------------------ > RUNIT TEST PROTOCOL -- Mon Dec 23 09:30:49 2024 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : metaMS RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 22.692 0.968 23.945
metaMS.Rcheck/metaMS-Ex.timings
name | user | system | elapsed | |
AnnotateTable | 0.042 | 0.000 | 0.041 | |
FEMsettings | 0.001 | 0.000 | 0.000 | |
addRI | 0.042 | 0.000 | 0.047 | |
alignmentLC | 0.085 | 0.032 | 0.117 | |
constructExpPseudoSpectra | 0.215 | 0.004 | 0.219 | |
createSTDdbGC | 0.000 | 0.002 | 0.002 | |
createSTDdbLC | 0.017 | 0.005 | 0.022 | |
errf | 0.019 | 0.000 | 0.019 | |
getAnnotationLC | 0.088 | 0.028 | 0.116 | |
getAnnotationMat | 0.038 | 0.000 | 0.038 | |
getFeatureInfo | 0.037 | 0.000 | 0.037 | |
getPeakTable | 0.070 | 0.044 | 0.114 | |
matchExpSpec | 0.018 | 0.000 | 0.019 | |
matchSamples2DB | 0.002 | 0.000 | 0.002 | |
matchSamples2Samples | 0.002 | 0.000 | 0.002 | |
metaMSsettings-class | 0.002 | 0.000 | 0.001 | |
metaSetting-methods | 0 | 0 | 0 | |
msp | 0.001 | 0.000 | 0.001 | |
peakDetection | 0.001 | 0.000 | 0.002 | |
plotPseudoSpectrum | 0.020 | 0.000 | 0.021 | |
processStandards | 0.037 | 0.000 | 0.037 | |
readStdInfo | 0.023 | 0.000 | 0.024 | |
runCAMERA | 1.239 | 0.096 | 1.337 | |
runGC | 0.036 | 0.000 | 0.036 | |
runLC | 0.021 | 0.000 | 0.021 | |
threeStdsDB | 0.012 | 0.000 | 0.011 | |
treat.DB | 0.004 | 0.000 | 0.004 | |