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This page was generated on 2025-11-11 12:02 -0500 (Tue, 11 Nov 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4902
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4638
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 1475/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
notameViz 1.0.0  (landing page)
Vilhelm Suksi
Snapshot Date: 2025-11-10 13:45 -0500 (Mon, 10 Nov 2025)
git_url: https://git.bioconductor.org/packages/notameViz
git_branch: RELEASE_3_22
git_last_commit: bb6e677
git_last_commit_date: 2025-10-29 11:38:35 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 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

CHECK results for notameViz on nebbiolo2

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.

raw results


Summary

Package: notameViz
Version: 1.0.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:notameViz.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings notameViz_1.0.0.tar.gz
StartedAt: 2025-11-11 02:22:06 -0500 (Tue, 11 Nov 2025)
EndedAt: 2025-11-11 02:27:07 -0500 (Tue, 11 Nov 2025)
EllapsedTime: 300.4 seconds
RetCode: 0
Status:   OK  
CheckDir: notameViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:notameViz.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings notameViz_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/notameViz.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘notameViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘notameViz’ version ‘1.0.0’
* 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 ‘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
plot_injection_lm    11.259  4.438   5.011
save_QC_plots        12.220  2.898  11.024
save_batch_plots      9.107  0.236   9.345
save_group_boxplots   7.698  0.299   7.999
save_group_lineplots  7.764  0.232   7.999
manhattan_plot        6.451  1.247   4.638
mz_rt_plot            4.656  1.513   2.771
plot_effect_heatmap   4.903  1.252   2.970
save_beeswarm_plots   5.945  0.112   6.045
volcano_plot          3.593  1.451   1.662
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/notameViz.Rcheck/00check.log’
for details.

Installation output

notameViz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL notameViz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘notameViz’ ...
** this is package ‘notameViz’ version ‘1.0.0’
** 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 version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 [2025-11-11 02:26:20] Saved to: /tmp/RtmpmEh9nv\test\recursive/file1cbc994f3c46e4.pdf
INFO [2025-11-11 02:26:20] Saved to: /tmp/RtmpmEh9nv/file1cbc9933ea166e.pdf
INFO [2025-11-11 02:26:20] Saved to: /tmp/RtmpmEh9nv/file1cbc996ae5f3df.emf
INFO [2025-11-11 02:26:20] Saved to: /tmp/RtmpmEh9nv/file1cbc99285307e2.svg
INFO [2025-11-11 02:26:21] Saved to: /tmp/RtmpmEh9nv/file1cbc997923e3cd.png
INFO [2025-11-11 02:26:21] Saved to: /tmp/RtmpmEh9nv/file1cbc995f5a5d87.tiff
INFO [2025-11-11 02:26:22] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-11 02:26:22] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-11 02:26:23] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-11 02:26:23] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-11 02:26:23] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-11 02:26:23] Saved line plots with mean line to: /tmp/RtmpmEh9nv\test\
INFO [2025-11-11 02:26:24] Saved to: /tmp/RtmpmEh9nv\test\/Glucose.emf
INFO [2025-11-11 02:26:24] Saved to: /tmp/RtmpmEh9nv\test\/Threoline.emf
INFO [2025-11-11 02:26:25] Saved to: /tmp/RtmpmEh9nv\test\/5-AVAB.emf
INFO [2025-11-11 02:26:25] Saved to: /tmp/RtmpmEh9nv\test\/1_2 acid.emf
INFO [2025-11-11 02:26:25] Saved to: /tmp/RtmpmEh9nv\test\/20_0 carbon chain.emf
INFO [2025-11-11 02:26:25] Saved line plots with mean line to: /tmp/RtmpmEh9nv\test\
INFO [2025-11-11 02:26:26] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-11 02:26:26] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-11 02:26:26] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-11 02:26:27] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-11 02:26:27] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-11 02:26:27] Saved group boxplots to: /tmp/RtmpmEh9nv\test\
INFO [2025-11-11 02:26:27] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-11 02:26:28] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-11 02:26:28] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-11 02:26:28] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-11 02:26:29] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-11 02:26:29] Saved group boxplots to: /tmp/RtmpmEh9nv\test\
INFO [2025-11-11 02:26:29] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-11 02:26:29] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-11 02:26:30] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-11 02:26:30] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-11 02:26:30] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-11 02:26:30] Saved beeswarm plots to: /tmp/RtmpmEh9nv\test\
INFO [2025-11-11 02:26:31] Saved to: /tmp/RtmpmEh9nv\test\/Glucose.emf
INFO [2025-11-11 02:26:31] Saved to: /tmp/RtmpmEh9nv\test\/Threoline.emf
INFO [2025-11-11 02:26:31] Saved to: /tmp/RtmpmEh9nv\test\/5-AVAB.emf
INFO [2025-11-11 02:26:31] Saved to: /tmp/RtmpmEh9nv\test\/1_2 acid.emf
INFO [2025-11-11 02:26:32] Saved to: /tmp/RtmpmEh9nv\test\/20_0 carbon chain.emf
INFO [2025-11-11 02:26:32] Saved beeswarm plots to: /tmp/RtmpmEh9nv\test\
INFO [2025-11-11 02:26:32] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-11 02:26:32] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-11 02:26:33] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-11 02:26:33] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-11 02:26:33] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-11 02:26:33] Saved scatter plots to: /tmp/RtmpmEh9nv\test\
INFO [2025-11-11 02:26:34] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-11 02:26:34] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-11 02:26:34] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-11 02:26:35] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-11 02:26:35] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-11 02:26:35] Saved scatter plots to: /tmp/RtmpmEh9nv\test\
INFO [2025-11-11 02:26:35] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-11 02:26:36] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-11 02:26:36] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-11 02:26:37] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-11 02:26:37] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-11 02:26:37] Saved line plots with mean line to: /tmp/RtmpmEh9nv\test\
INFO [2025-11-11 02:26:38] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-11 02:26:38] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-11 02:26:39] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-11 02:26:39] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-11 02:26:40] Saved to: /tmp/RtmpmEh9nv\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-11 02:26:40] Saved line plots with mean line to: /tmp/RtmpmEh9nv\test\
INFO [2025-11-11 02:26:41] 
Saved batch plots to: /tmp/RtmpmEh9nv\test\batch_plots.pdf
INFO [2025-11-11 02:26:41] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-11 02:26:41] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-11 02:26:41] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-11 02:26:41] 
92% of features flagged for low quality
INFO [2025-11-11 02:26:41] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-11 02:26:41] 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 
 28.933   1.322  30.251

Example timings

notameViz.Rcheck/notameViz-Ex.timings

nameusersystemelapsed
manhattan_plot6.4511.2474.638
mz_rt_plot4.6561.5132.771
plot_dendrogram0.5250.0570.582
plot_dist_density1.4090.4591.358
plot_effect_heatmap4.9031.2522.970
plot_injection_lm11.259 4.438 5.011
plot_p_histogram3.5451.3861.675
plot_pca0.4450.0330.478
plot_pca_arrows0.8790.0590.940
plot_pca_hexbin0.2670.0320.299
plot_pca_loadings0.3140.0170.332
plot_quality1.4320.0521.485
plot_sample_boxplots1.1640.0421.205
plot_sample_heatmap0.6790.0280.708
plot_tsne0.5050.0220.527
plot_tsne_arrows0.9090.0550.963
plot_tsne_hexbin0.2790.0020.281
save_QC_plots12.220 2.89811.024
save_batch_plots9.1070.2369.345
save_beeswarm_plots5.9450.1126.045
save_dc_plots3.0910.6793.080
save_group_boxplots7.6980.2997.999
save_group_lineplots7.7640.2327.999
save_plot0.7160.0100.727
save_scatter_plots3.3520.0433.397
save_subject_line_plots3.6690.2863.956
visualize_clusters2.0200.0432.064
volcano_plot3.5931.4511.662