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This page was generated on 2025-10-15 12:05 -0400 (Wed, 15 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4866
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4653
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4598
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4610
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 1465/2346HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
notameViz 0.99.5  (landing page)
Vilhelm Suksi
Snapshot Date: 2025-10-14 13:45 -0400 (Tue, 14 Oct 2025)
git_url: https://git.bioconductor.org/packages/notameViz
git_branch: devel
git_last_commit: 2a2d418
git_last_commit_date: 2025-10-03 05:08:08 -0400 (Fri, 03 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

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: 0.99.5
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_0.99.5.tar.gz
StartedAt: 2025-10-14 23:57:23 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-15 00:02:55 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 331.9 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_0.99.5.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 ‘0.99.5’
* 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        13.815  3.411  13.315
save_group_lineplots 12.860  0.173  13.112
plot_injection_lm     8.085  4.422   4.658
save_batch_plots     11.151  0.171  11.371
plot_effect_heatmap   6.724  2.331   4.148
save_group_boxplots   7.571  0.089   7.689
manhattan_plot        6.172  1.469   4.929
save_beeswarm_plots   5.933  0.159   6.130
volcano_plot          3.176  2.336   1.992
mz_rt_plot            4.079  1.414   2.995
* 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 ‘0.99.5’
** 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 [2025-10-15 00:02:18] Saved to: /tmp/RtmpVdH4Ih\test\recursive/filee8f175d5df67.pdf
INFO [2025-10-15 00:02:18] Saved to: /tmp/RtmpVdH4Ih/filee8f15b6e0fc1.pdf
INFO [2025-10-15 00:02:18] Saved to: /tmp/RtmpVdH4Ih/filee8f1302fd320.emf
INFO [2025-10-15 00:02:18] Saved to: /tmp/RtmpVdH4Ih/filee8f1aac79ea.svg
INFO [2025-10-15 00:02:18] Saved to: /tmp/RtmpVdH4Ih/filee8f15c733bc9.png
INFO [2025-10-15 00:02:19] Saved to: /tmp/RtmpVdH4Ih/filee8f12c62cfcf.tiff
2025-10-15 00:02:19.774 R[59633:544732143] XType: com.apple.fonts is not accessible.
2025-10-15 00:02:19.774 R[59633:544732143] XType: XTFontStaticRegistry is enabled.
INFO [2025-10-15 00:02:20] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-15 00:02:20] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-15 00:02:21] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-15 00:02:21] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-15 00:02:21] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-15 00:02:21] Saved line plots with mean line to: /tmp/RtmpVdH4Ih\test\
INFO [2025-10-15 00:02:22] Saved to: /tmp/RtmpVdH4Ih\test\/Glucose.emf
INFO [2025-10-15 00:02:22] Saved to: /tmp/RtmpVdH4Ih\test\/Threoline.emf
INFO [2025-10-15 00:02:22] Saved to: /tmp/RtmpVdH4Ih\test\/5-AVAB.emf
INFO [2025-10-15 00:02:23] Saved to: /tmp/RtmpVdH4Ih\test\/1_2 acid.emf
INFO [2025-10-15 00:02:23] Saved to: /tmp/RtmpVdH4Ih\test\/20_0 carbon chain.emf
INFO [2025-10-15 00:02:23] Saved line plots with mean line to: /tmp/RtmpVdH4Ih\test\
INFO [2025-10-15 00:02:24] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-15 00:02:24] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-15 00:02:24] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-15 00:02:25] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-15 00:02:26] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-15 00:02:26] Saved group boxplots to: /tmp/RtmpVdH4Ih\test\
INFO [2025-10-15 00:02:26] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-15 00:02:26] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-15 00:02:27] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-15 00:02:27] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-15 00:02:27] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-15 00:02:27] Saved group boxplots to: /tmp/RtmpVdH4Ih\test\
INFO [2025-10-15 00:02:28] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-15 00:02:28] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-15 00:02:28] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-15 00:02:28] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-15 00:02:29] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-15 00:02:29] Saved beeswarm plots to: /tmp/RtmpVdH4Ih\test\
INFO [2025-10-15 00:02:29] Saved to: /tmp/RtmpVdH4Ih\test\/Glucose.emf
INFO [2025-10-15 00:02:29] Saved to: /tmp/RtmpVdH4Ih\test\/Threoline.emf
INFO [2025-10-15 00:02:30] Saved to: /tmp/RtmpVdH4Ih\test\/5-AVAB.emf
INFO [2025-10-15 00:02:30] Saved to: /tmp/RtmpVdH4Ih\test\/1_2 acid.emf
INFO [2025-10-15 00:02:30] Saved to: /tmp/RtmpVdH4Ih\test\/20_0 carbon chain.emf
INFO [2025-10-15 00:02:30] Saved beeswarm plots to: /tmp/RtmpVdH4Ih\test\
INFO [2025-10-15 00:02:30] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-15 00:02:31] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-15 00:02:31] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-15 00:02:31] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-15 00:02:32] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-15 00:02:32] Saved scatter plots to: /tmp/RtmpVdH4Ih\test\
INFO [2025-10-15 00:02:32] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-15 00:02:32] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-15 00:02:33] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-15 00:02:33] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-15 00:02:33] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-15 00:02:33] Saved scatter plots to: /tmp/RtmpVdH4Ih\test\
INFO [2025-10-15 00:02:34] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-15 00:02:35] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-15 00:02:35] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-15 00:02:36] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-15 00:02:37] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-15 00:02:37] Saved line plots with mean line to: /tmp/RtmpVdH4Ih\test\
INFO [2025-10-15 00:02:37] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-10-15 00:02:38] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-10-15 00:02:38] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-10-15 00:02:39] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-10-15 00:02:40] Saved to: /tmp/RtmpVdH4Ih\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-10-15 00:02:40] Saved line plots with mean line to: /tmp/RtmpVdH4Ih\test\
INFO [2025-10-15 00:02:41] 
Saved batch plots to: /tmp/RtmpVdH4Ih\test\batch_plots.pdf
INFO [2025-10-15 00:02:41] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-15 00:02:41] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-15 00:02:41] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-15 00:02:41] 
92% of features flagged for low quality
INFO [2025-10-15 00:02:41] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-10-15 00:02:41] 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 
 32.936   1.082  34.265

Example timings

notameViz.Rcheck/notameViz-Ex.timings

nameusersystemelapsed
manhattan_plot6.1721.4694.929
mz_rt_plot4.0791.4142.995
plot_dendrogram0.5890.0320.629
plot_dist_density1.9630.9251.860
plot_effect_heatmap6.7242.3314.148
plot_injection_lm8.0854.4224.658
plot_p_histogram2.8691.6381.814
plot_pca0.4340.0190.458
plot_pca_arrows0.9710.0361.029
plot_pca_hexbin0.4430.0150.461
plot_pca_loadings0.3970.0080.408
plot_quality1.7130.0241.755
plot_sample_boxplots1.3810.0151.404
plot_sample_heatmap0.8010.0180.839
plot_tsne0.5330.0140.553
plot_tsne_arrows1.0180.0131.037
plot_tsne_hexbin0.5070.0120.528
save_QC_plots13.815 3.41113.315
save_batch_plots11.151 0.17111.371
save_beeswarm_plots5.9330.1596.130
save_dc_plots3.0230.6263.003
save_group_boxplots7.5710.0897.689
save_group_lineplots12.860 0.17313.112
save_plot0.7630.0110.779
save_scatter_plots3.4990.0293.547
save_subject_line_plots3.3220.0253.362
visualize_clusters2.6760.0362.726
volcano_plot3.1762.3361.992