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This page was generated on 2025-12-04 12:02 -0500 (Thu, 04 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4878
merida1macOS 12.7.6 Montereyx86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4624
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: 2025-12-01 13:45 -0500 (Mon, 01 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: notameViz
Version: 1.0.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:notameViz.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings notameViz_1.0.0.tar.gz
StartedAt: 2025-12-02 12:35:00 -0000 (Tue, 02 Dec 2025)
EndedAt: 2025-12-02 12:42:13 -0000 (Tue, 02 Dec 2025)
EllapsedTime: 433.1 seconds
RetCode: 0
Status:   OK  
CheckDir: notameViz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:notameViz.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings notameViz_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/notameViz.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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
save_QC_plots        18.175  3.413  16.432
plot_injection_lm    15.824  5.356   7.137
save_batch_plots     13.479  0.124  13.756
save_group_boxplots  11.680  0.295  12.020
save_group_lineplots 10.601  0.076  10.716
manhattan_plot        8.480  1.593   6.872
plot_effect_heatmap   7.985  1.931   5.147
mz_rt_plot            6.954  2.243   4.760
save_beeswarm_plots   8.492  0.103   8.717
plot_p_histogram      5.255  1.983   2.651
volcano_plot          4.966  1.669   2.191
save_scatter_plots    5.479  0.212   5.776
save_dc_plots         3.996  1.011   4.002
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/notameViz.Rcheck/00check.log’
for details.

Installation output

notameViz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL notameViz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 [2025-12-02 12:41:37] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\recursive/file32a959798edc09.pdf
INFO [2025-12-02 12:41:38] Saved to: /home/biocbuild/tmp/RtmpozD7aH/file32a95922d3d0b8.pdf
INFO [2025-12-02 12:41:38] Saved to: /home/biocbuild/tmp/RtmpozD7aH/file32a95946958641.emf
INFO [2025-12-02 12:41:38] Saved to: /home/biocbuild/tmp/RtmpozD7aH/file32a9591a4228fa.svg
INFO [2025-12-02 12:41:38] Saved to: /home/biocbuild/tmp/RtmpozD7aH/file32a959656f9b6c.png
INFO [2025-12-02 12:41:38] Saved to: /home/biocbuild/tmp/RtmpozD7aH/file32a9592ddf4530.tiff
INFO [2025-12-02 12:41:39] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-02 12:41:40] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-02 12:41:41] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-02 12:41:41] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-02 12:41:42] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-02 12:41:42] Saved line plots with mean line to: /home/biocbuild/tmp/RtmpozD7aH\test\
INFO [2025-12-02 12:41:42] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/Glucose.emf
INFO [2025-12-02 12:41:43] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/Threoline.emf
INFO [2025-12-02 12:41:43] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/5-AVAB.emf
INFO [2025-12-02 12:41:44] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/1_2 acid.emf
INFO [2025-12-02 12:41:44] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/20_0 carbon chain.emf
INFO [2025-12-02 12:41:44] Saved line plots with mean line to: /home/biocbuild/tmp/RtmpozD7aH\test\
INFO [2025-12-02 12:41:45] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-02 12:41:45] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-02 12:41:46] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-02 12:41:46] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-02 12:41:47] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-02 12:41:47] Saved group boxplots to: /home/biocbuild/tmp/RtmpozD7aH\test\
INFO [2025-12-02 12:41:47] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-02 12:41:48] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-02 12:41:48] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-02 12:41:49] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-02 12:41:49] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-02 12:41:49] Saved group boxplots to: /home/biocbuild/tmp/RtmpozD7aH\test\
INFO [2025-12-02 12:41:50] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-02 12:41:50] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-02 12:41:50] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-02 12:41:51] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-02 12:41:51] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-02 12:41:51] Saved beeswarm plots to: /home/biocbuild/tmp/RtmpozD7aH\test\
INFO [2025-12-02 12:41:52] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/Glucose.emf
INFO [2025-12-02 12:41:52] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/Threoline.emf
INFO [2025-12-02 12:41:52] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/5-AVAB.emf
INFO [2025-12-02 12:41:53] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/1_2 acid.emf
INFO [2025-12-02 12:41:53] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/20_0 carbon chain.emf
INFO [2025-12-02 12:41:53] Saved beeswarm plots to: /home/biocbuild/tmp/RtmpozD7aH\test\
INFO [2025-12-02 12:41:54] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-02 12:41:54] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-02 12:41:55] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-02 12:41:55] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-02 12:41:56] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-02 12:41:56] Saved scatter plots to: /home/biocbuild/tmp/RtmpozD7aH\test\
INFO [2025-12-02 12:41:56] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-02 12:41:57] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-02 12:41:57] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-02 12:41:58] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-02 12:41:58] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-02 12:41:58] Saved scatter plots to: /home/biocbuild/tmp/RtmpozD7aH\test\
INFO [2025-12-02 12:41:59] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-02 12:41:59] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-02 12:42:00] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-02 12:42:01] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-02 12:42:01] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-02 12:42:01] Saved line plots with mean line to: /home/biocbuild/tmp/RtmpozD7aH\test\
INFO [2025-12-02 12:42:02] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-12-02 12:42:03] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-12-02 12:42:03] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-12-02 12:42:04] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-12-02 12:42:05] Saved to: /home/biocbuild/tmp/RtmpozD7aH\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-12-02 12:42:05] Saved line plots with mean line to: /home/biocbuild/tmp/RtmpozD7aH\test\
INFO [2025-12-02 12:42:06] 
Saved batch plots to: /home/biocbuild/tmp/RtmpozD7aH\test\batch_plots.pdf
INFO [2025-12-02 12:42:06] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-12-02 12:42:07] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-12-02 12:42:07] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-12-02 12:42:07] 
92% of features flagged for low quality
INFO [2025-12-02 12:42:07] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-12-02 12:42:07] 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 
 39.938   0.950  40.997

Example timings

notameViz.Rcheck/notameViz-Ex.timings

nameusersystemelapsed
manhattan_plot8.4801.5936.872
mz_rt_plot6.9542.2434.760
plot_dendrogram0.7390.0480.792
plot_dist_density2.1510.6332.059
plot_effect_heatmap7.9851.9315.147
plot_injection_lm15.824 5.356 7.137
plot_p_histogram5.2551.9832.651
plot_pca0.6270.0280.657
plot_pca_arrows1.3230.1791.508
plot_pca_hexbin0.3630.0240.388
plot_pca_loadings0.4610.0080.472
plot_quality2.1030.0532.349
plot_sample_boxplots1.7860.0711.953
plot_sample_heatmap0.9660.0190.991
plot_tsne0.6980.0150.720
plot_tsne_arrows1.3840.0161.403
plot_tsne_hexbin0.4360.0080.446
save_QC_plots18.175 3.41316.432
save_batch_plots13.479 0.12413.756
save_beeswarm_plots8.4920.1038.717
save_dc_plots3.9961.0114.002
save_group_boxplots11.680 0.29512.020
save_group_lineplots10.601 0.07610.716
save_plot1.0990.0151.136
save_scatter_plots5.4790.2125.776
save_subject_line_plots3.9210.1404.073
visualize_clusters2.9560.0643.027
volcano_plot4.9661.6692.191