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This page was generated on 2025-10-23 12:05 -0400 (Thu, 23 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4894
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4684
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4629
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 1470/2355HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
notameViz 0.99.6  (landing page)
Vilhelm Suksi
Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025)
git_url: https://git.bioconductor.org/packages/notameViz
git_branch: devel
git_last_commit: 47f9fcb
git_last_commit_date: 2025-10-20 03:10:48 -0400 (Mon, 20 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  YES
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  

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: 0.99.6
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_0.99.6.tar.gz
StartedAt: 2025-10-22 22:51:17 -0400 (Wed, 22 Oct 2025)
EndedAt: 2025-10-22 22:56:24 -0400 (Wed, 22 Oct 2025)
EllapsedTime: 307.5 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_0.99.6.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 ‘0.99.6’
* 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
save_QC_plots        15.080  3.827  13.043
plot_injection_lm    13.032  5.345   5.741
save_group_lineplots 11.392  0.138  11.569
save_batch_plots     10.161  0.079  10.289
manhattan_plot        7.707  1.518   5.091
plot_effect_heatmap   6.439  1.973   3.875
mz_rt_plot            5.880  1.812   3.257
save_group_boxplots   7.154  0.085   7.259
volcano_plot          4.612  2.151   2.168
save_beeswarm_plots   6.439  0.229   6.701
plot_p_histogram      4.505  1.816   2.061
* 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 ‘0.99.6’
** 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 [2025-10-22 22:55:49] Saved to: /tmp/RtmpXd4OpU\test\recursive/file452c3c443152.pdf
INFO [2025-10-22 22:55:49] Saved to: /tmp/RtmpXd4OpU/file452c241e13f5.pdf
INFO [2025-10-22 22:55:49] Saved to: /tmp/RtmpXd4OpU/file452c4a87934.emf
INFO [2025-10-22 22:55:50] Saved to: /tmp/RtmpXd4OpU/file452c4beeb722.svg
INFO [2025-10-22 22:55:50] Saved to: /tmp/RtmpXd4OpU/file452c231212ff.png
INFO [2025-10-22 22:55:50] Saved to: /tmp/RtmpXd4OpU/file452c2dde4f99.tiff
2025-10-22 22:55:50.958 R[17708:618299517] XType: com.apple.fonts is not accessible.
2025-10-22 22:55:50.958 R[17708:618299517] XType: XTFontStaticRegistry is enabled.
INFO [2025-10-22 22:55:51] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-22 22:55:51] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-22 22:55:52] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-22 22:55:52] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-22 22:55:52] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-22 22:55:52] Saved line plots with mean line to: /tmp/RtmpXd4OpU\test\
INFO [2025-10-22 22:55:53] Saved to: /tmp/RtmpXd4OpU\test\/Glucose.emf
INFO [2025-10-22 22:55:53] Saved to: /tmp/RtmpXd4OpU\test\/Threoline.emf
INFO [2025-10-22 22:55:53] Saved to: /tmp/RtmpXd4OpU\test\/5-AVAB.emf
INFO [2025-10-22 22:55:54] Saved to: /tmp/RtmpXd4OpU\test\/1_2 acid.emf
INFO [2025-10-22 22:55:54] Saved to: /tmp/RtmpXd4OpU\test\/20_0 carbon chain.emf
INFO [2025-10-22 22:55:54] Saved line plots with mean line to: /tmp/RtmpXd4OpU\test\
INFO [2025-10-22 22:55:54] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-22 22:55:55] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-22 22:55:55] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-22 22:55:56] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-22 22:55:56] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-22 22:55:56] Saved group boxplots to: /tmp/RtmpXd4OpU\test\
INFO [2025-10-22 22:55:57] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-22 22:55:57] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-22 22:55:57] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-22 22:55:58] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-22 22:55:58] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-22 22:55:58] Saved group boxplots to: /tmp/RtmpXd4OpU\test\
INFO [2025-10-22 22:55:58] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-22 22:55:59] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-22 22:55:59] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-22 22:55:59] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-22 22:55:59] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-22 22:55:59] Saved beeswarm plots to: /tmp/RtmpXd4OpU\test\
INFO [2025-10-22 22:56:00] Saved to: /tmp/RtmpXd4OpU\test\/Glucose.emf
INFO [2025-10-22 22:56:00] Saved to: /tmp/RtmpXd4OpU\test\/Threoline.emf
INFO [2025-10-22 22:56:00] Saved to: /tmp/RtmpXd4OpU\test\/5-AVAB.emf
INFO [2025-10-22 22:56:00] Saved to: /tmp/RtmpXd4OpU\test\/1_2 acid.emf
INFO [2025-10-22 22:56:01] Saved to: /tmp/RtmpXd4OpU\test\/20_0 carbon chain.emf
INFO [2025-10-22 22:56:01] Saved beeswarm plots to: /tmp/RtmpXd4OpU\test\
INFO [2025-10-22 22:56:01] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-22 22:56:01] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-22 22:56:02] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-22 22:56:02] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-22 22:56:02] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-22 22:56:02] Saved scatter plots to: /tmp/RtmpXd4OpU\test\
INFO [2025-10-22 22:56:03] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-22 22:56:03] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-22 22:56:03] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-22 22:56:03] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-22 22:56:04] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-22 22:56:04] Saved scatter plots to: /tmp/RtmpXd4OpU\test\
INFO [2025-10-22 22:56:05] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-22 22:56:05] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-22 22:56:06] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-22 22:56:06] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-22 22:56:07] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-22 22:56:07] Saved line plots with mean line to: /tmp/RtmpXd4OpU\test\
INFO [2025-10-22 22:56:08] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-22 22:56:08] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-22 22:56:09] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-22 22:56:09] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-22 22:56:10] Saved to: /tmp/RtmpXd4OpU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-22 22:56:10] Saved line plots with mean line to: /tmp/RtmpXd4OpU\test\
INFO [2025-10-22 22:56:11] 
Saved batch plots to: /tmp/RtmpXd4OpU\test\batch_plots.pdf
INFO [2025-10-22 22:56:11] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-22 22:56:11] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-22 22:56:11] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-22 22:56:12] 
92% of features flagged for low quality
INFO [2025-10-22 22:56:12] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-22 22:56:12] 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 
 31.144   0.938  32.254

Example timings

notameViz.Rcheck/notameViz-Ex.timings

nameusersystemelapsed
manhattan_plot7.7071.5185.091
mz_rt_plot5.8801.8123.257
plot_dendrogram0.5580.0290.589
plot_dist_density1.6690.4841.539
plot_effect_heatmap6.4391.9733.875
plot_injection_lm13.032 5.345 5.741
plot_p_histogram4.5051.8162.061
plot_pca0.4100.0150.428
plot_pca_arrows0.9620.0140.979
plot_pca_hexbin0.4240.0120.438
plot_pca_loadings0.3680.0070.377
plot_quality1.5280.0141.545
plot_sample_boxplots1.3030.0141.321
plot_sample_heatmap0.7490.0100.762
plot_tsne0.4890.0100.500
plot_tsne_arrows0.8730.0090.884
plot_tsne_hexbin0.3990.0060.405
save_QC_plots15.080 3.82713.043
save_batch_plots10.161 0.07910.289
save_beeswarm_plots6.4390.2296.701
save_dc_plots2.8070.5732.754
save_group_boxplots7.1540.0857.259
save_group_lineplots11.392 0.13811.569
save_plot0.6820.0100.694
save_scatter_plots3.1860.0293.237
save_subject_line_plots2.9710.0213.006
visualize_clusters2.3920.0332.445
volcano_plot4.6122.1512.168