Vilhelm Suksi
| Snapshot Date: 2025-11-24 13:45 -0500 (Mon, 24 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-27 12:04 -0500 (Thu, 27 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4876 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4656 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4602 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 1475/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| notameViz 1.0.0 (landing page) Vilhelm Suksi
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | NA | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: 1.0.0 |
| 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: 2025-11-26 17:45:05 -0500 (Wed, 26 Nov 2025) |
| EndedAt: 2025-11-26 17:53:56 -0500 (Wed, 26 Nov 2025) |
| EllapsedTime: 530.6 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/notameViz.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
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 ‘1.0.0’
* 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 12.118 4.565 9.336
save_QC_plots 13.946 2.652 18.469
save_group_lineplots 15.024 0.354 27.106
save_batch_plots 10.298 0.108 16.882
manhattan_plot 8.461 1.327 11.874
save_group_boxplots 9.510 0.137 17.888
save_beeswarm_plots 7.031 0.119 10.973
mz_rt_plot 5.286 1.487 5.575
plot_effect_heatmap 5.210 1.515 5.791
plot_p_histogram 3.968 1.508 3.095
volcano_plot 3.911 1.501 3.048
save_dc_plots 3.310 0.784 5.507
* 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.
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-arm64/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)
notameViz.Rcheck/tests/testthat.Rout
R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 [2025-11-26 17:53:01] Saved to: /tmp/Rtmp8FVecU\test\recursive/file60ee3b9bce56.pdf
INFO [2025-11-26 17:53:01] Saved to: /tmp/Rtmp8FVecU/file60eef60cb97.pdf
INFO [2025-11-26 17:53:01] Saved to: /tmp/Rtmp8FVecU/file60ee3e3d175c.emf
INFO [2025-11-26 17:53:01] Saved to: /tmp/Rtmp8FVecU/file60ee2f45bde4.svg
INFO [2025-11-26 17:53:01] Saved to: /tmp/Rtmp8FVecU/file60ee4f674a3a.png
INFO [2025-11-26 17:53:01] Saved to: /tmp/Rtmp8FVecU/file60ee3fe24bbb.tiff
2025-11-26 17:53:02.800 R[24814:97843196] XType: Using static font registry.
INFO [2025-11-26 17:53:03] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-26 17:53:03] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-26 17:53:04] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-26 17:53:04] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-26 17:53:05] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-26 17:53:05] Saved line plots with mean line to: /tmp/Rtmp8FVecU\test\
INFO [2025-11-26 17:53:05] Saved to: /tmp/Rtmp8FVecU\test\/Glucose.emf
INFO [2025-11-26 17:53:06] Saved to: /tmp/Rtmp8FVecU\test\/Threoline.emf
INFO [2025-11-26 17:53:06] Saved to: /tmp/Rtmp8FVecU\test\/5-AVAB.emf
INFO [2025-11-26 17:53:07] Saved to: /tmp/Rtmp8FVecU\test\/1_2 acid.emf
INFO [2025-11-26 17:53:07] Saved to: /tmp/Rtmp8FVecU\test\/20_0 carbon chain.emf
INFO [2025-11-26 17:53:07] Saved line plots with mean line to: /tmp/Rtmp8FVecU\test\
INFO [2025-11-26 17:53:08] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-26 17:53:08] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-26 17:53:09] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-26 17:53:09] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-26 17:53:09] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-26 17:53:09] Saved group boxplots to: /tmp/Rtmp8FVecU\test\
INFO [2025-11-26 17:53:10] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-26 17:53:10] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-26 17:53:11] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-26 17:53:11] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-26 17:53:12] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-26 17:53:12] Saved group boxplots to: /tmp/Rtmp8FVecU\test\
INFO [2025-11-26 17:53:13] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-26 17:53:13] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-26 17:53:13] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-26 17:53:14] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-26 17:53:14] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-26 17:53:14] Saved beeswarm plots to: /tmp/Rtmp8FVecU\test\
INFO [2025-11-26 17:53:15] Saved to: /tmp/Rtmp8FVecU\test\/Glucose.emf
INFO [2025-11-26 17:53:15] Saved to: /tmp/Rtmp8FVecU\test\/Threoline.emf
INFO [2025-11-26 17:53:16] Saved to: /tmp/Rtmp8FVecU\test\/5-AVAB.emf
INFO [2025-11-26 17:53:16] Saved to: /tmp/Rtmp8FVecU\test\/1_2 acid.emf
INFO [2025-11-26 17:53:17] Saved to: /tmp/Rtmp8FVecU\test\/20_0 carbon chain.emf
INFO [2025-11-26 17:53:17] Saved beeswarm plots to: /tmp/Rtmp8FVecU\test\
INFO [2025-11-26 17:53:17] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-26 17:53:18] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-26 17:53:18] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-26 17:53:19] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-26 17:53:19] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-26 17:53:19] Saved scatter plots to: /tmp/Rtmp8FVecU\test\
INFO [2025-11-26 17:53:19] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-26 17:53:20] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-26 17:53:20] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-26 17:53:21] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-26 17:53:21] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-26 17:53:21] Saved scatter plots to: /tmp/Rtmp8FVecU\test\
INFO [2025-11-26 17:53:23] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-26 17:53:24] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-26 17:53:25] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-26 17:53:27] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-26 17:53:28] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-26 17:53:28] Saved line plots with mean line to: /tmp/Rtmp8FVecU\test\
INFO [2025-11-26 17:53:29] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-26 17:53:30] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-26 17:53:30] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-26 17:53:31] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-26 17:53:32] Saved to: /tmp/Rtmp8FVecU\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-26 17:53:32] Saved line plots with mean line to: /tmp/Rtmp8FVecU\test\
INFO [2025-11-26 17:53:34]
Saved batch plots to: /tmp/Rtmp8FVecU\test\batch_plots.pdf
INFO [2025-11-26 17:53:34] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-26 17:53:34] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-26 17:53:34] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-26 17:53:35]
92% of features flagged for low quality
INFO [2025-11-26 17:53:35] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-26 17:53:35] 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
32.804 0.970 51.739
notameViz.Rcheck/notameViz-Ex.timings
| name | user | system | elapsed | |
| manhattan_plot | 8.461 | 1.327 | 11.874 | |
| mz_rt_plot | 5.286 | 1.487 | 5.575 | |
| plot_dendrogram | 0.585 | 0.038 | 1.239 | |
| plot_dist_density | 1.691 | 0.486 | 2.527 | |
| plot_effect_heatmap | 5.210 | 1.515 | 5.791 | |
| plot_injection_lm | 12.118 | 4.565 | 9.336 | |
| plot_p_histogram | 3.968 | 1.508 | 3.095 | |
| plot_pca | 0.430 | 0.033 | 0.767 | |
| plot_pca_arrows | 0.874 | 0.016 | 1.456 | |
| plot_pca_hexbin | 0.382 | 0.013 | 0.908 | |
| plot_pca_loadings | 0.350 | 0.008 | 0.580 | |
| plot_quality | 1.544 | 0.018 | 2.820 | |
| plot_sample_boxplots | 1.226 | 0.018 | 2.258 | |
| plot_sample_heatmap | 0.743 | 0.013 | 1.200 | |
| plot_tsne | 0.508 | 0.015 | 0.761 | |
| plot_tsne_arrows | 0.925 | 0.015 | 1.534 | |
| plot_tsne_hexbin | 0.418 | 0.012 | 0.736 | |
| save_QC_plots | 13.946 | 2.652 | 18.469 | |
| save_batch_plots | 10.298 | 0.108 | 16.882 | |
| save_beeswarm_plots | 7.031 | 0.119 | 10.973 | |
| save_dc_plots | 3.310 | 0.784 | 5.507 | |
| save_group_boxplots | 9.510 | 0.137 | 17.888 | |
| save_group_lineplots | 15.024 | 0.354 | 27.106 | |
| save_plot | 0.698 | 0.012 | 1.098 | |
| save_scatter_plots | 3.001 | 0.039 | 4.750 | |
| save_subject_line_plots | 2.951 | 0.031 | 4.533 | |
| visualize_clusters | 2.265 | 0.032 | 3.722 | |
| volcano_plot | 3.911 | 1.501 | 3.048 | |