Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-15 12:07 -0400 (Wed, 15 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4866 |
lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4653 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4598 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4610 |
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 1465/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
notameViz 0.99.5 (landing page) Vilhelm Suksi
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the notameViz package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/notameViz.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: notameViz |
Version: 0.99.5 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:notameViz.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings notameViz_0.99.5.tar.gz |
StartedAt: 2025-10-14 10:52:47 -0000 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 10:59:48 -0000 (Tue, 14 Oct 2025) |
EllapsedTime: 420.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: notameViz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:notameViz.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings notameViz_0.99.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/notameViz.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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 ‘notameViz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘notameViz’ version ‘0.99.5’ * 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 ‘notameViz’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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: save_dc_plots.Rd: correct_drift 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed save_QC_plots 15.873 2.262 19.572 save_batch_plots 12.761 0.052 17.335 plot_injection_lm 7.869 2.646 6.995 save_group_boxplots 10.022 0.043 10.608 save_group_lineplots 9.194 0.004 9.885 plot_effect_heatmap 7.739 1.366 7.122 save_beeswarm_plots 8.392 0.337 9.602 manhattan_plot 5.733 0.962 6.592 save_dc_plots 4.189 1.715 5.891 mz_rt_plot 4.691 0.879 5.608 visualize_clusters 3.906 1.363 5.207 * 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/notameViz.Rcheck/00check.log’ for details.
notameViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL notameViz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘notameViz’ ... ** this is package ‘notameViz’ version ‘0.99.5’ ** using staged installation ** R ** 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 (notameViz)
notameViz.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 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. > library(testthat) > library(notameViz) Loading required package: ggplot2 Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics 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 Loading required package: S4Vectors 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: IRanges Loading required package: Seqinfo 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")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > > test_check("notameViz") Running tests in parallel requires the 3rd edition INFO [2025-10-14 10:59:00] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\recursive/file26838c6d4ec642.pdf INFO [2025-10-14 10:59:01] Saved to: /home/biocbuild/tmp/RtmpZOOfpk/file26838c5fa226a3.pdf INFO [2025-10-14 10:59:01] Saved to: /home/biocbuild/tmp/RtmpZOOfpk/file26838c13c10474.emf INFO [2025-10-14 10:59:01] Saved to: /home/biocbuild/tmp/RtmpZOOfpk/file26838c240a1b66.svg INFO [2025-10-14 10:59:01] Saved to: /home/biocbuild/tmp/RtmpZOOfpk/file26838c296bb090.png INFO [2025-10-14 10:59:01] Saved to: /home/biocbuild/tmp/RtmpZOOfpk/file26838c383249b3.tiff INFO [2025-10-14 10:59:02] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_259_9623a4_4322.emf INFO [2025-10-14 10:59:03] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_108_1065a2_6121.emf INFO [2025-10-14 10:59:04] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_158_23a1_4128.emf INFO [2025-10-14 10:59:05] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_251_0056a0_6161.emf INFO [2025-10-14 10:59:06] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_401_52a4_211.emf INFO [2025-10-14 10:59:06] Saved line plots with mean line to: /home/biocbuild/tmp/RtmpZOOfpk\test\ INFO [2025-10-14 10:59:07] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/Glucose.emf INFO [2025-10-14 10:59:07] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/Threoline.emf INFO [2025-10-14 10:59:07] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/5-AVAB.emf INFO [2025-10-14 10:59:08] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/1_2 acid.emf INFO [2025-10-14 10:59:09] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/20_0 carbon chain.emf INFO [2025-10-14 10:59:09] Saved line plots with mean line to: /home/biocbuild/tmp/RtmpZOOfpk\test\ INFO [2025-10-14 10:59:10] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_259_9623a4_4322.emf INFO [2025-10-14 10:59:11] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_108_1065a2_6121.emf INFO [2025-10-14 10:59:12] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_158_23a1_4128.emf INFO [2025-10-14 10:59:13] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_251_0056a0_6161.emf INFO [2025-10-14 10:59:13] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_401_52a4_211.emf INFO [2025-10-14 10:59:13] Saved group boxplots to: /home/biocbuild/tmp/RtmpZOOfpk\test\ INFO [2025-10-14 10:59:14] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_259_9623a4_4322.emf INFO [2025-10-14 10:59:14] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_108_1065a2_6121.emf INFO [2025-10-14 10:59:15] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_158_23a1_4128.emf INFO [2025-10-14 10:59:15] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_251_0056a0_6161.emf INFO [2025-10-14 10:59:16] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_401_52a4_211.emf INFO [2025-10-14 10:59:16] Saved group boxplots to: /home/biocbuild/tmp/RtmpZOOfpk\test\ INFO [2025-10-14 10:59:17] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_259_9623a4_4322.emf INFO [2025-10-14 10:59:17] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_108_1065a2_6121.emf INFO [2025-10-14 10:59:17] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_158_23a1_4128.emf INFO [2025-10-14 10:59:18] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_251_0056a0_6161.emf INFO [2025-10-14 10:59:19] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_401_52a4_211.emf INFO [2025-10-14 10:59:19] Saved beeswarm plots to: /home/biocbuild/tmp/RtmpZOOfpk\test\ INFO [2025-10-14 10:59:19] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/Glucose.emf INFO [2025-10-14 10:59:20] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/Threoline.emf INFO [2025-10-14 10:59:20] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/5-AVAB.emf INFO [2025-10-14 10:59:20] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/1_2 acid.emf INFO [2025-10-14 10:59:21] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/20_0 carbon chain.emf INFO [2025-10-14 10:59:21] Saved beeswarm plots to: /home/biocbuild/tmp/RtmpZOOfpk\test\ INFO [2025-10-14 10:59:21] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_259_9623a4_4322.emf INFO [2025-10-14 10:59:22] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_108_1065a2_6121.emf INFO [2025-10-14 10:59:22] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_158_23a1_4128.emf INFO [2025-10-14 10:59:23] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_251_0056a0_6161.emf INFO [2025-10-14 10:59:23] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_401_52a4_211.emf INFO [2025-10-14 10:59:23] Saved scatter plots to: /home/biocbuild/tmp/RtmpZOOfpk\test\ INFO [2025-10-14 10:59:24] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_259_9623a4_4322.emf INFO [2025-10-14 10:59:24] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_108_1065a2_6121.emf INFO [2025-10-14 10:59:25] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_158_23a1_4128.emf INFO [2025-10-14 10:59:25] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_251_0056a0_6161.emf INFO [2025-10-14 10:59:26] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_401_52a4_211.emf INFO [2025-10-14 10:59:26] Saved scatter plots to: /home/biocbuild/tmp/RtmpZOOfpk\test\ INFO [2025-10-14 10:59:27] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_259_9623a4_4322.emf INFO [2025-10-14 10:59:27] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_108_1065a2_6121.emf INFO [2025-10-14 10:59:28] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_158_23a1_4128.emf INFO [2025-10-14 10:59:29] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_251_0056a0_6161.emf INFO [2025-10-14 10:59:29] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_401_52a4_211.emf INFO [2025-10-14 10:59:29] Saved line plots with mean line to: /home/biocbuild/tmp/RtmpZOOfpk\test\ INFO [2025-10-14 10:59:30] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_259_9623a4_4322.emf INFO [2025-10-14 10:59:31] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_108_1065a2_6121.emf INFO [2025-10-14 10:59:31] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_158_23a1_4128.emf INFO [2025-10-14 10:59:32] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_251_0056a0_6161.emf INFO [2025-10-14 10:59:33] Saved to: /home/biocbuild/tmp/RtmpZOOfpk\test\/HILIC_neg_401_52a4_211.emf INFO [2025-10-14 10:59:33] Saved line plots with mean line to: /home/biocbuild/tmp/RtmpZOOfpk\test\ INFO [2025-10-14 10:59:34] Saved batch plots to: /home/biocbuild/tmp/RtmpZOOfpk\test\batch_plots.pdf INFO [2025-10-14 10:59:34] Identified m/z column Average_Mz and retention time column Average_Rt_min INFO [2025-10-14 10:59:35] Identified m/z column Average_Mz and retention time column Average_Rt_min INFO [2025-10-14 10:59:35] Identified m/z column Average_Mz and retention time column Average_Rt_min INFO [2025-10-14 10:59:38] 92% of features flagged for low quality INFO [2025-10-14 10:59:39] Identified m/z column Average_Mz and retention time column Average_Rt_min INFO [2025-10-14 10:59:39] Identified m/z column Average_Mz and retention time column Average_Rt_min [ FAIL 0 | WARN 182 | SKIP 0 | PASS 26 ] [ FAIL 0 | WARN 182 | SKIP 0 | PASS 26 ] > > proc.time() user system elapsed 42.024 1.325 52.499
notameViz.Rcheck/notameViz-Ex.timings
name | user | system | elapsed | |
manhattan_plot | 5.733 | 0.962 | 6.592 | |
mz_rt_plot | 4.691 | 0.879 | 5.608 | |
plot_dendrogram | 0.775 | 0.032 | 0.874 | |
plot_dist_density | 2.684 | 1.519 | 3.519 | |
plot_effect_heatmap | 7.739 | 1.366 | 7.122 | |
plot_injection_lm | 7.869 | 2.646 | 6.995 | |
plot_p_histogram | 2.590 | 0.855 | 2.139 | |
plot_pca | 0.522 | 0.029 | 0.558 | |
plot_pca_arrows | 1.227 | 0.020 | 1.397 | |
plot_pca_hexbin | 0.319 | 0.012 | 0.331 | |
plot_pca_loadings | 0.435 | 0.015 | 0.492 | |
plot_quality | 2.417 | 0.504 | 3.104 | |
plot_sample_boxplots | 1.605 | 0.032 | 1.694 | |
plot_sample_heatmap | 0.980 | 0.003 | 1.260 | |
plot_tsne | 0.657 | 0.017 | 1.352 | |
plot_tsne_arrows | 1.330 | 0.014 | 2.697 | |
plot_tsne_hexbin | 0.391 | 0.004 | 0.490 | |
save_QC_plots | 15.873 | 2.262 | 19.572 | |
save_batch_plots | 12.761 | 0.052 | 17.335 | |
save_beeswarm_plots | 8.392 | 0.337 | 9.602 | |
save_dc_plots | 4.189 | 1.715 | 5.891 | |
save_group_boxplots | 10.022 | 0.043 | 10.608 | |
save_group_lineplots | 9.194 | 0.004 | 9.885 | |
save_plot | 0.935 | 0.005 | 0.956 | |
save_scatter_plots | 4.127 | 0.028 | 4.551 | |
save_subject_line_plots | 4.143 | 0.008 | 4.656 | |
visualize_clusters | 3.906 | 1.363 | 5.207 | |
volcano_plot | 2.422 | 0.884 | 1.844 | |