Vilhelm Suksi
| Snapshot Date: 2025-11-20 13:40 -0500 (Thu, 20 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/notameViz |
| git_branch: devel |
| git_last_commit: 1590e89 |
| git_last_commit_date: 2025-10-29 11:38:35 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-21 11:38 -0500 (Fri, 21 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4829 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4602 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4566 |
| 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 1457/2327 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| notameViz 1.1.0 (landing page) Vilhelm Suksi
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: notameViz |
| Version: 1.1.0 |
| 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_1.1.0.tar.gz |
| StartedAt: 2025-11-20 22:52:32 -0500 (Thu, 20 Nov 2025) |
| EndedAt: 2025-11-20 22:58:03 -0500 (Thu, 20 Nov 2025) |
| EllapsedTime: 331.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: notameViz.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/notameViz.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* 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 Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘notameViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘notameViz’ version ‘1.1.0’
* 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 15.054 6.941 6.802
save_QC_plots 15.146 3.785 13.481
save_group_lineplots 15.345 0.350 15.796
save_batch_plots 10.315 0.086 10.464
manhattan_plot 7.994 1.682 5.455
save_group_boxplots 9.193 0.114 9.362
plot_effect_heatmap 6.447 2.180 3.837
mz_rt_plot 6.204 2.163 3.464
plot_p_histogram 4.916 2.158 2.297
volcano_plot 4.642 2.077 2.105
save_beeswarm_plots 6.613 0.089 6.739
save_dc_plots 3.898 1.653 3.644
* 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-3.23-bioc/meat/notameViz.Rcheck/00check.log’
for details.
notameViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL notameViz ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library’ * installing *source* package ‘notameViz’ ... ** this is package ‘notameViz’ version ‘1.1.0’ ** 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)
notameViz.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
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 [2025-11-20 22:57:27] Saved to: /tmp/Rtmp6PLvzT\test\recursive/file13e0a6e218c46.pdf
INFO [2025-11-20 22:57:27] Saved to: /tmp/Rtmp6PLvzT/file13e0a601544f3.pdf
INFO [2025-11-20 22:57:27] Saved to: /tmp/Rtmp6PLvzT/file13e0a3c993e51.emf
INFO [2025-11-20 22:57:27] Saved to: /tmp/Rtmp6PLvzT/file13e0a6d752251.svg
INFO [2025-11-20 22:57:27] Saved to: /tmp/Rtmp6PLvzT/file13e0a35f46dac.png
INFO [2025-11-20 22:57:27] Saved to: /tmp/Rtmp6PLvzT/file13e0a499455e.tiff
2025-11-20 22:57:28.494 R[81418:59259590] XType: Using static font registry.
INFO [2025-11-20 22:57:28] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-20 22:57:29] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-20 22:57:29] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-20 22:57:30] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-20 22:57:30] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-20 22:57:30] Saved line plots with mean line to: /tmp/Rtmp6PLvzT\test\
INFO [2025-11-20 22:57:31] Saved to: /tmp/Rtmp6PLvzT\test\/Glucose.emf
INFO [2025-11-20 22:57:31] Saved to: /tmp/Rtmp6PLvzT\test\/Threoline.emf
INFO [2025-11-20 22:57:31] Saved to: /tmp/Rtmp6PLvzT\test\/5-AVAB.emf
INFO [2025-11-20 22:57:31] Saved to: /tmp/Rtmp6PLvzT\test\/1_2 acid.emf
INFO [2025-11-20 22:57:32] Saved to: /tmp/Rtmp6PLvzT\test\/20_0 carbon chain.emf
INFO [2025-11-20 22:57:32] Saved line plots with mean line to: /tmp/Rtmp6PLvzT\test\
INFO [2025-11-20 22:57:32] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-20 22:57:33] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-20 22:57:33] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-20 22:57:34] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-20 22:57:34] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-20 22:57:34] Saved group boxplots to: /tmp/Rtmp6PLvzT\test\
INFO [2025-11-20 22:57:35] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-20 22:57:35] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-20 22:57:35] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-20 22:57:36] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-20 22:57:36] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-20 22:57:36] Saved group boxplots to: /tmp/Rtmp6PLvzT\test\
INFO [2025-11-20 22:57:36] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-20 22:57:36] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-20 22:57:37] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-20 22:57:37] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-20 22:57:37] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-20 22:57:37] Saved beeswarm plots to: /tmp/Rtmp6PLvzT\test\
INFO [2025-11-20 22:57:37] Saved to: /tmp/Rtmp6PLvzT\test\/Glucose.emf
INFO [2025-11-20 22:57:38] Saved to: /tmp/Rtmp6PLvzT\test\/Threoline.emf
INFO [2025-11-20 22:57:38] Saved to: /tmp/Rtmp6PLvzT\test\/5-AVAB.emf
INFO [2025-11-20 22:57:38] Saved to: /tmp/Rtmp6PLvzT\test\/1_2 acid.emf
INFO [2025-11-20 22:57:38] Saved to: /tmp/Rtmp6PLvzT\test\/20_0 carbon chain.emf
INFO [2025-11-20 22:57:38] Saved beeswarm plots to: /tmp/Rtmp6PLvzT\test\
INFO [2025-11-20 22:57:39] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-20 22:57:39] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-20 22:57:39] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-20 22:57:40] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-20 22:57:40] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-20 22:57:40] Saved scatter plots to: /tmp/Rtmp6PLvzT\test\
INFO [2025-11-20 22:57:40] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-20 22:57:41] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-20 22:57:41] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-20 22:57:41] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-20 22:57:42] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-20 22:57:42] Saved scatter plots to: /tmp/Rtmp6PLvzT\test\
INFO [2025-11-20 22:57:43] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-20 22:57:43] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-20 22:57:44] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-20 22:57:44] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-20 22:57:45] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-20 22:57:45] Saved line plots with mean line to: /tmp/Rtmp6PLvzT\test\
INFO [2025-11-20 22:57:46] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-20 22:57:46] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-20 22:57:47] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-20 22:57:47] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-20 22:57:48] Saved to: /tmp/Rtmp6PLvzT\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-20 22:57:48] Saved line plots with mean line to: /tmp/Rtmp6PLvzT\test\
INFO [2025-11-20 22:57:49]
Saved batch plots to: /tmp/Rtmp6PLvzT\test\batch_plots.pdf
INFO [2025-11-20 22:57:49] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-20 22:57:50] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-20 22:57:50] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-20 22:57:50]
92% of features flagged for low quality
INFO [2025-11-20 22:57:50] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-20 22:57:50] 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
32.508 1.177 34.093
notameViz.Rcheck/notameViz-Ex.timings
| name | user | system | elapsed | |
| manhattan_plot | 7.994 | 1.682 | 5.455 | |
| mz_rt_plot | 6.204 | 2.163 | 3.464 | |
| plot_dendrogram | 0.563 | 0.029 | 0.595 | |
| plot_dist_density | 1.854 | 0.590 | 1.695 | |
| plot_effect_heatmap | 6.447 | 2.180 | 3.837 | |
| plot_injection_lm | 15.054 | 6.941 | 6.802 | |
| plot_p_histogram | 4.916 | 2.158 | 2.297 | |
| plot_pca | 0.504 | 0.029 | 0.539 | |
| plot_pca_arrows | 1.038 | 0.018 | 1.067 | |
| plot_pca_hexbin | 0.450 | 0.014 | 0.467 | |
| plot_pca_loadings | 0.346 | 0.008 | 0.356 | |
| plot_quality | 1.658 | 0.014 | 1.681 | |
| plot_sample_boxplots | 1.366 | 0.016 | 1.389 | |
| plot_sample_heatmap | 0.802 | 0.012 | 0.819 | |
| plot_tsne | 0.526 | 0.011 | 0.542 | |
| plot_tsne_arrows | 0.974 | 0.011 | 0.989 | |
| plot_tsne_hexbin | 0.396 | 0.007 | 0.405 | |
| save_QC_plots | 15.146 | 3.785 | 13.481 | |
| save_batch_plots | 10.315 | 0.086 | 10.464 | |
| save_beeswarm_plots | 6.613 | 0.089 | 6.739 | |
| save_dc_plots | 3.898 | 1.653 | 3.644 | |
| save_group_boxplots | 9.193 | 0.114 | 9.362 | |
| save_group_lineplots | 15.345 | 0.350 | 15.796 | |
| save_plot | 0.722 | 0.010 | 0.736 | |
| save_scatter_plots | 3.233 | 0.041 | 3.309 | |
| save_subject_line_plots | 3.292 | 0.041 | 3.369 | |
| visualize_clusters | 2.362 | 0.037 | 2.420 | |
| volcano_plot | 4.642 | 2.077 | 2.105 | |