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This page was generated on 2025-11-04 12:04 -0500 (Tue, 04 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
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4692
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: 2025-11-03 13:45 -0500 (Mon, 03 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
lconwaymacOS 12.7.6 Monterey / x86_64  OK    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 lconway

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: 2025-11-03 22:59:39 -0500 (Mon, 03 Nov 2025)
EndedAt: 2025-11-03 23:04:48 -0500 (Mon, 03 Nov 2025)
EllapsedTime: 309.5 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 4.5.1 Patched (2025-09-10 r88807)
* 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    13.241  5.744   5.889
save_QC_plots        14.612  3.925  12.704
save_group_lineplots 13.604  0.292  13.961
save_batch_plots      9.813  0.068   9.916
save_group_boxplots   8.693  0.100   8.831
manhattan_plot        7.264  1.427   4.944
plot_effect_heatmap   6.322  2.195   4.050
mz_rt_plot            5.834  1.916   3.252
save_beeswarm_plots   6.555  0.086   6.675
volcano_plot          4.398  2.044   2.011
plot_p_histogram      4.499  1.934   2.093
* 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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 [2025-11-03 23:04:13] Saved to: /tmp/RtmpgZG8ik\test\recursive/filef94b7f9d67b.pdf
INFO [2025-11-03 23:04:13] Saved to: /tmp/RtmpgZG8ik/filef94bbaa7169.pdf
INFO [2025-11-03 23:04:13] Saved to: /tmp/RtmpgZG8ik/filef94b65de42bd.emf
INFO [2025-11-03 23:04:13] Saved to: /tmp/RtmpgZG8ik/filef94b10516d96.svg
INFO [2025-11-03 23:04:13] Saved to: /tmp/RtmpgZG8ik/filef94b2d3528ca.png
INFO [2025-11-03 23:04:13] Saved to: /tmp/RtmpgZG8ik/filef94b140608de.tiff
2025-11-03 23:04:14.332 R[63819:725604669] XType: com.apple.fonts is not accessible.
2025-11-03 23:04:14.332 R[63819:725604669] XType: XTFontStaticRegistry is enabled.
INFO [2025-11-03 23:04:14] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-03 23:04:15] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-03 23:04:15] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-03 23:04:15] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-03 23:04:16] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-03 23:04:16] Saved line plots with mean line to: /tmp/RtmpgZG8ik\test\
INFO [2025-11-03 23:04:16] Saved to: /tmp/RtmpgZG8ik\test\/Glucose.emf
INFO [2025-11-03 23:04:16] Saved to: /tmp/RtmpgZG8ik\test\/Threoline.emf
INFO [2025-11-03 23:04:17] Saved to: /tmp/RtmpgZG8ik\test\/5-AVAB.emf
INFO [2025-11-03 23:04:17] Saved to: /tmp/RtmpgZG8ik\test\/1_2 acid.emf
INFO [2025-11-03 23:04:17] Saved to: /tmp/RtmpgZG8ik\test\/20_0 carbon chain.emf
INFO [2025-11-03 23:04:17] Saved line plots with mean line to: /tmp/RtmpgZG8ik\test\
INFO [2025-11-03 23:04:18] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-03 23:04:18] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-03 23:04:18] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-03 23:04:19] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-03 23:04:19] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-03 23:04:19] Saved group boxplots to: /tmp/RtmpgZG8ik\test\
INFO [2025-11-03 23:04:20] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-03 23:04:20] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-03 23:04:20] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-03 23:04:21] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-03 23:04:21] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-03 23:04:21] Saved group boxplots to: /tmp/RtmpgZG8ik\test\
INFO [2025-11-03 23:04:21] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-03 23:04:21] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-03 23:04:22] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-03 23:04:22] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-03 23:04:22] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-03 23:04:22] Saved beeswarm plots to: /tmp/RtmpgZG8ik\test\
INFO [2025-11-03 23:04:23] Saved to: /tmp/RtmpgZG8ik\test\/Glucose.emf
INFO [2025-11-03 23:04:23] Saved to: /tmp/RtmpgZG8ik\test\/Threoline.emf
INFO [2025-11-03 23:04:23] Saved to: /tmp/RtmpgZG8ik\test\/5-AVAB.emf
INFO [2025-11-03 23:04:23] Saved to: /tmp/RtmpgZG8ik\test\/1_2 acid.emf
INFO [2025-11-03 23:04:24] Saved to: /tmp/RtmpgZG8ik\test\/20_0 carbon chain.emf
INFO [2025-11-03 23:04:24] Saved beeswarm plots to: /tmp/RtmpgZG8ik\test\
INFO [2025-11-03 23:04:24] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-03 23:04:24] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-03 23:04:25] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-03 23:04:25] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-03 23:04:25] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-03 23:04:25] Saved scatter plots to: /tmp/RtmpgZG8ik\test\
INFO [2025-11-03 23:04:26] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-03 23:04:26] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-03 23:04:26] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-03 23:04:26] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-03 23:04:27] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-03 23:04:27] Saved scatter plots to: /tmp/RtmpgZG8ik\test\
INFO [2025-11-03 23:04:28] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-03 23:04:29] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-03 23:04:29] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-03 23:04:30] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-03 23:04:30] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-03 23:04:30] Saved line plots with mean line to: /tmp/RtmpgZG8ik\test\
INFO [2025-11-03 23:04:31] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-03 23:04:32] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-03 23:04:33] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-03 23:04:33] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-03 23:04:34] Saved to: /tmp/RtmpgZG8ik\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-03 23:04:34] Saved line plots with mean line to: /tmp/RtmpgZG8ik\test\
INFO [2025-11-03 23:04:35] 
Saved batch plots to: /tmp/RtmpgZG8ik\test\batch_plots.pdf
INFO [2025-11-03 23:04:35] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-03 23:04:35] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-03 23:04:35] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-03 23:04:35] 
92% of features flagged for low quality
INFO [2025-11-03 23:04:35] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-03 23:04:36] 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 
 32.075   0.982  33.247

Example timings

notameViz.Rcheck/notameViz-Ex.timings

nameusersystemelapsed
manhattan_plot7.2641.4274.944
mz_rt_plot5.8341.9163.252
plot_dendrogram0.5160.0290.546
plot_dist_density1.6780.5241.533
plot_effect_heatmap6.3222.1954.050
plot_injection_lm13.241 5.744 5.889
plot_p_histogram4.4991.9342.093
plot_pca0.4510.0210.475
plot_pca_arrows0.9010.0130.917
plot_pca_hexbin0.3880.0130.402
plot_pca_loadings0.3780.0090.388
plot_quality1.5390.0141.559
plot_sample_boxplots1.2870.0161.308
plot_sample_heatmap0.7180.0120.735
plot_tsne0.5060.0120.523
plot_tsne_arrows0.9800.0090.994
plot_tsne_hexbin0.4110.0080.422
save_QC_plots14.612 3.92512.704
save_batch_plots9.8130.0689.916
save_beeswarm_plots6.5550.0866.675
save_dc_plots3.2670.8963.159
save_group_boxplots8.6930.1008.831
save_group_lineplots13.604 0.29213.961
save_plot0.6230.0100.634
save_scatter_plots3.0850.0283.132
save_subject_line_plots3.0590.0253.101
visualize_clusters2.3980.0282.439
volcano_plot4.3982.0442.011