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This page was generated on 2026-04-20 11:37 -0400 (Mon, 20 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 alpha (2026-04-05 r89794) 4961
kjohnson3macOS 13.7.7 Venturaarm644.6.0 alpha (2026-04-08 r89818) 4690
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4627
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 1499/2404HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
notameViz 1.1.4  (landing page)
Vilhelm Suksi
Snapshot Date: 2026-04-19 13:40 -0400 (Sun, 19 Apr 2026)
git_url: https://git.bioconductor.org/packages/notameViz
git_branch: devel
git_last_commit: 7604681
git_last_commit_date: 2026-02-17 01:29:32 -0400 (Tue, 17 Feb 2026)
nebbiolo1Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  
See other builds for notameViz in R Universe.

CHECK results for notameViz on kunpeng2

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.

raw results


Summary

Package: notameViz
Version: 1.1.4
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_1.1.4.tar.gz
StartedAt: 2026-04-17 05:11:55 -0000 (Fri, 17 Apr 2026)
EndedAt: 2026-04-17 05:18:13 -0000 (Fri, 17 Apr 2026)
EllapsedTime: 378.3 seconds
RetCode: 0
Status:   OK  
CheckDir: notameViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.1.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/notameViz.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘notameViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘notameViz’ version ‘1.1.4’
* 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        13.199  0.187  13.426
save_batch_plots     12.624  0.096  12.758
save_group_boxplots  11.191  0.231  11.452
save_group_lineplots 10.375  0.363  10.764
manhattan_plot        8.731  1.428   5.954
plot_effect_heatmap   7.371  1.766   4.664
mz_rt_plot            6.690  1.627   3.951
save_beeswarm_plots   7.897  0.031   7.951
plot_p_histogram      4.583  1.557   2.073
volcano_plot          4.549  1.522   2.000
save_scatter_plots    5.184  0.364   5.559
* 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-3.23-bioc/meat/notameViz.Rcheck/00check.log’
for details.

Installation output

notameViz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL notameViz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘notameViz’ ...
** this is package ‘notameViz’ version ‘1.1.4’
** 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)

Tests output

notameViz.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
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 [2026-04-17 05:17:38] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\recursive/file2093c4185ea322.pdf
INFO [2026-04-17 05:17:38] Saved to: /home/biocbuild/tmp/RtmpakiG8V/file2093c467e5444d.pdf
INFO [2026-04-17 05:17:38] Saved to: /home/biocbuild/tmp/RtmpakiG8V/file2093c48fa97e.emf
INFO [2026-04-17 05:17:38] Saved to: /home/biocbuild/tmp/RtmpakiG8V/file2093c439c24364.svg
INFO [2026-04-17 05:17:38] Saved to: /home/biocbuild/tmp/RtmpakiG8V/file2093c4778a09e9.png
INFO [2026-04-17 05:17:39] Saved to: /home/biocbuild/tmp/RtmpakiG8V/file2093c433bed5b2.tiff
INFO [2026-04-17 05:17:40] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2026-04-17 05:17:41] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2026-04-17 05:17:41] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_158_23a1_4128.emf
INFO [2026-04-17 05:17:42] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2026-04-17 05:17:42] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_401_52a4_211.emf
INFO [2026-04-17 05:17:42] Saved line plots with mean line to: /home/biocbuild/tmp/RtmpakiG8V\test\
INFO [2026-04-17 05:17:43] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/Glucose.emf
INFO [2026-04-17 05:17:43] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/Threoline.emf
INFO [2026-04-17 05:17:44] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/5-AVAB.emf
INFO [2026-04-17 05:17:44] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/1_2 acid.emf
INFO [2026-04-17 05:17:44] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/20_0 carbon chain.emf
INFO [2026-04-17 05:17:44] Saved line plots with mean line to: /home/biocbuild/tmp/RtmpakiG8V\test\
INFO [2026-04-17 05:17:45] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2026-04-17 05:17:46] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2026-04-17 05:17:46] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_158_23a1_4128.emf
INFO [2026-04-17 05:17:47] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2026-04-17 05:17:47] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_401_52a4_211.emf
INFO [2026-04-17 05:17:47] Saved group boxplots to: /home/biocbuild/tmp/RtmpakiG8V\test\
INFO [2026-04-17 05:17:48] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2026-04-17 05:17:48] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2026-04-17 05:17:49] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_158_23a1_4128.emf
INFO [2026-04-17 05:17:49] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2026-04-17 05:17:50] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_401_52a4_211.emf
INFO [2026-04-17 05:17:50] Saved group boxplots to: /home/biocbuild/tmp/RtmpakiG8V\test\
INFO [2026-04-17 05:17:50] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2026-04-17 05:17:50] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2026-04-17 05:17:51] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_158_23a1_4128.emf
INFO [2026-04-17 05:17:51] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2026-04-17 05:17:52] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_401_52a4_211.emf
INFO [2026-04-17 05:17:52] Saved beeswarm plots to: /home/biocbuild/tmp/RtmpakiG8V\test\
INFO [2026-04-17 05:17:52] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/Glucose.emf
INFO [2026-04-17 05:17:53] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/Threoline.emf
INFO [2026-04-17 05:17:53] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/5-AVAB.emf
INFO [2026-04-17 05:17:53] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/1_2 acid.emf
INFO [2026-04-17 05:17:54] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/20_0 carbon chain.emf
INFO [2026-04-17 05:17:54] Saved beeswarm plots to: /home/biocbuild/tmp/RtmpakiG8V\test\
INFO [2026-04-17 05:17:54] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2026-04-17 05:17:55] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2026-04-17 05:17:55] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_158_23a1_4128.emf
INFO [2026-04-17 05:17:56] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2026-04-17 05:17:56] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_401_52a4_211.emf
INFO [2026-04-17 05:17:56] Saved scatter plots to: /home/biocbuild/tmp/RtmpakiG8V\test\
INFO [2026-04-17 05:17:57] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2026-04-17 05:17:57] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2026-04-17 05:17:58] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_158_23a1_4128.emf
INFO [2026-04-17 05:17:58] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2026-04-17 05:17:58] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_401_52a4_211.emf
INFO [2026-04-17 05:17:58] Saved scatter plots to: /home/biocbuild/tmp/RtmpakiG8V\test\
INFO [2026-04-17 05:17:59] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2026-04-17 05:18:00] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2026-04-17 05:18:01] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_158_23a1_4128.emf
INFO [2026-04-17 05:18:01] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2026-04-17 05:18:02] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_401_52a4_211.emf
INFO [2026-04-17 05:18:02] Saved line plots with mean line to: /home/biocbuild/tmp/RtmpakiG8V\test\
INFO [2026-04-17 05:18:03] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2026-04-17 05:18:03] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2026-04-17 05:18:04] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_158_23a1_4128.emf
INFO [2026-04-17 05:18:04] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2026-04-17 05:18:05] Saved to: /home/biocbuild/tmp/RtmpakiG8V\test\/HILIC_neg_401_52a4_211.emf
INFO [2026-04-17 05:18:05] Saved line plots with mean line to: /home/biocbuild/tmp/RtmpakiG8V\test\
INFO [2026-04-17 05:18:07] 
Saved batch plots to: /home/biocbuild/tmp/RtmpakiG8V\test\batch_plots.pdf
INFO [2026-04-17 05:18:07] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2026-04-17 05:18:07] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2026-04-17 05:18:07] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2026-04-17 05:18:07] 
92% of features flagged for low quality
INFO [2026-04-17 05:18:07] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2026-04-17 05:18:07] 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 
 40.443   1.338  41.877

Example timings

notameViz.Rcheck/notameViz-Ex.timings

nameusersystemelapsed
manhattan_plot8.7311.4285.954
mz_rt_plot6.6901.6273.951
plot_dendrogram0.7140.0830.800
plot_dist_density2.1080.6082.019
plot_effect_heatmap7.3711.7664.664
plot_injection_lm3.3230.2163.549
plot_p_histogram4.5831.5572.073
plot_pca0.5710.0440.618
plot_pca_arrows1.2680.1031.376
plot_pca_hexbin0.3100.0200.331
plot_pca_loadings0.4760.0120.489
plot_quality2.0700.0962.172
plot_sample_boxplots1.7250.0561.786
plot_sample_heatmap0.9440.0591.006
plot_tsne0.6650.0120.679
plot_tsne_arrows1.2220.0121.238
plot_tsne_hexbin0.3890.0040.394
save_QC_plots13.199 0.18713.426
save_batch_plots12.624 0.09612.758
save_beeswarm_plots7.8970.0317.951
save_dc_plots3.8650.6623.715
save_group_boxplots11.191 0.23111.452
save_group_lineplots10.375 0.36310.764
save_plot1.0370.0271.066
save_scatter_plots5.1840.3645.559
save_subject_line_plots3.8760.1043.989
visualize_clusters3.0170.0593.084
volcano_plot4.5491.5222.000