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This page was generated on 2025-12-08 12:01 -0500 (Mon, 08 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4879
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4668
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4669
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: 2025-12-04 13:45 -0500 (Thu, 04 Dec 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
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for notameViz on merida1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:notameViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings notameViz_1.0.0.tar.gz
StartedAt: 2025-12-05 08:59:39 -0500 (Fri, 05 Dec 2025)
EndedAt: 2025-12-05 09:11:36 -0500 (Fri, 05 Dec 2025)
EllapsedTime: 716.9 seconds
RetCode: 0
Status:   OK  
CheckDir: notameViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:notameViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings notameViz_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/notameViz.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘notameViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘notameViz’ version ‘1.0.0’
* 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 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       25.561 10.040  14.833
save_QC_plots           29.251  4.767  30.435
save_group_lineplots    29.522  0.590  37.166
save_batch_plots        21.367  0.127  24.585
save_group_boxplots     17.981  0.176  21.981
plot_effect_heatmap     13.903  3.408  10.454
manhattan_plot          13.495  2.911  10.259
mz_rt_plot              12.029  3.569   8.995
save_beeswarm_plots     13.474  0.133  16.500
plot_p_histogram         8.606  3.305   5.079
volcano_plot             8.431  3.386   4.865
save_dc_plots            7.098  1.454   7.976
save_scatter_plots       6.828  0.043   8.771
save_subject_line_plots  6.551  0.034   7.973
visualize_clusters       5.118  0.046   6.317
* 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
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/notameViz.Rcheck/00check.log’
for details.

Installation output

notameViz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL notameViz
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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(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 [2025-12-05 09:10:13] Saved to: /tmp/Rtmp6morNe\test\recursive/file12d4f55bb4f1f.pdf
INFO [2025-12-05 09:10:14] Saved to: /tmp/Rtmp6morNe/file12d4f76ad91f3.pdf
INFO [2025-12-05 09:10:14] Saved to: /tmp/Rtmp6morNe/file12d4f108ed8b8.emf
INFO [2025-12-05 09:10:15] Saved to: /tmp/Rtmp6morNe/file12d4f7abc3917.svg
INFO [2025-12-05 09:10:15] Saved to: /tmp/Rtmp6morNe/file12d4f4c162227.png
INFO [2025-12-05 09:10:15] Saved to: /tmp/Rtmp6morNe/file12d4f2113ef10.tiff
2025-12-05 09:10:17.706 R[77135:92875205] XType: com.apple.fonts is not accessible.
2025-12-05 09:10:17.706 R[77135:92875205] XType: XTFontStaticRegistry is enabled.
INFO [2025-12-05 09:10:18] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-05 09:10:20] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-05 09:10:21] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-05 09:10:22] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-05 09:10:23] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-05 09:10:23] Saved line plots with mean line to: /tmp/Rtmp6morNe\test\
INFO [2025-12-05 09:10:24] Saved to: /tmp/Rtmp6morNe\test\/Glucose.emf
INFO [2025-12-05 09:10:25] Saved to: /tmp/Rtmp6morNe\test\/Threoline.emf
INFO [2025-12-05 09:10:25] Saved to: /tmp/Rtmp6morNe\test\/5-AVAB.emf
INFO [2025-12-05 09:10:26] Saved to: /tmp/Rtmp6morNe\test\/1_2 acid.emf
INFO [2025-12-05 09:10:27] Saved to: /tmp/Rtmp6morNe\test\/20_0 carbon chain.emf
INFO [2025-12-05 09:10:27] Saved line plots with mean line to: /tmp/Rtmp6morNe\test\
INFO [2025-12-05 09:10:28] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-05 09:10:29] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-05 09:10:30] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-05 09:10:31] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-05 09:10:32] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-05 09:10:32] Saved group boxplots to: /tmp/Rtmp6morNe\test\
INFO [2025-12-05 09:10:33] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-05 09:10:34] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-05 09:10:34] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-05 09:10:35] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-05 09:10:36] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-05 09:10:36] Saved group boxplots to: /tmp/Rtmp6morNe\test\
INFO [2025-12-05 09:10:37] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-05 09:10:38] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-05 09:10:39] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-05 09:10:39] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-05 09:10:40] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-05 09:10:40] Saved beeswarm plots to: /tmp/Rtmp6morNe\test\
INFO [2025-12-05 09:10:41] Saved to: /tmp/Rtmp6morNe\test\/Glucose.emf
INFO [2025-12-05 09:10:42] Saved to: /tmp/Rtmp6morNe\test\/Threoline.emf
INFO [2025-12-05 09:10:42] Saved to: /tmp/Rtmp6morNe\test\/5-AVAB.emf
INFO [2025-12-05 09:10:43] Saved to: /tmp/Rtmp6morNe\test\/1_2 acid.emf
INFO [2025-12-05 09:10:44] Saved to: /tmp/Rtmp6morNe\test\/20_0 carbon chain.emf
INFO [2025-12-05 09:10:44] Saved beeswarm plots to: /tmp/Rtmp6morNe\test\
INFO [2025-12-05 09:10:45] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-05 09:10:46] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-05 09:10:46] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-05 09:10:47] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-05 09:10:48] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-05 09:10:48] Saved scatter plots to: /tmp/Rtmp6morNe\test\
INFO [2025-12-05 09:10:49] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-05 09:10:50] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-05 09:10:51] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-05 09:10:51] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-05 09:10:52] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-05 09:10:52] Saved scatter plots to: /tmp/Rtmp6morNe\test\
INFO [2025-12-05 09:10:55] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-05 09:10:56] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-05 09:10:58] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-05 09:11:01] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-05 09:11:02] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-05 09:11:02] Saved line plots with mean line to: /tmp/Rtmp6morNe\test\
INFO [2025-12-05 09:11:04] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-05 09:11:06] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-05 09:11:07] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-05 09:11:09] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-05 09:11:10] Saved to: /tmp/Rtmp6morNe\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-05 09:11:10] Saved line plots with mean line to: /tmp/Rtmp6morNe\test\
INFO [2025-12-05 09:11:13] 
Saved batch plots to: /tmp/Rtmp6morNe\test\batch_plots.pdf
INFO [2025-12-05 09:11:13] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-12-05 09:11:13] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-12-05 09:11:14] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-12-05 09:11:14] 
92% of features flagged for low quality
INFO [2025-12-05 09:11:14] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-12-05 09:11:15] Identified m/z column Average_Mz and retention time column Average_Rt_min
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 26 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
 63.340   1.823  85.277

Example timings

notameViz.Rcheck/notameViz-Ex.timings

nameusersystemelapsed
manhattan_plot13.495 2.91110.259
mz_rt_plot12.029 3.569 8.995
plot_dendrogram1.2260.0521.630
plot_dist_density3.7230.9254.110
plot_effect_heatmap13.903 3.40810.454
plot_injection_lm25.56110.04014.833
plot_p_histogram8.6063.3055.079
plot_pca0.9370.0571.248
plot_pca_arrows2.1020.0262.716
plot_pca_hexbin0.8580.0211.103
plot_pca_loadings0.7600.0141.061
plot_quality3.3790.0304.211
plot_sample_boxplots2.7930.0263.543
plot_sample_heatmap1.6580.0202.101
plot_tsne1.0940.0171.385
plot_tsne_arrows2.0100.0162.473
plot_tsne_hexbin0.8730.0091.162
save_QC_plots29.251 4.76730.435
save_batch_plots21.367 0.12724.585
save_beeswarm_plots13.474 0.13316.500
save_dc_plots7.0981.4547.976
save_group_boxplots17.981 0.17621.981
save_group_lineplots29.522 0.59037.166
save_plot1.5990.0202.109
save_scatter_plots6.8280.0438.771
save_subject_line_plots6.5510.0347.973
visualize_clusters5.1180.0466.317
volcano_plot8.4313.3864.865