Vilhelm Suksi
| Snapshot Date: 2025-11-09 13:40 -0500 (Sun, 09 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 Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-10 11:32 -0500 (Mon, 10 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" | 4821 |
| 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 1453/2323 | 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 | | ||||||||
|
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: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:notameViz.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings notameViz_1.1.0.tar.gz |
| StartedAt: 2025-11-10 01:58:13 -0500 (Mon, 10 Nov 2025) |
| EndedAt: 2025-11-10 02:03:11 -0500 (Mon, 10 Nov 2025) |
| EllapsedTime: 297.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: notameViz.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:notameViz.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings notameViz_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/notameViz.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* 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 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
plot_injection_lm 11.406 5.047 5.224
save_QC_plots 11.572 2.532 10.606
save_batch_plots 9.134 0.116 9.252
save_group_boxplots 7.876 0.185 8.065
manhattan_plot 6.447 1.542 4.829
save_group_lineplots 7.702 0.090 7.792
mz_rt_plot 4.777 1.862 3.124
plot_effect_heatmap 4.975 1.539 3.239
save_beeswarm_plots 5.942 0.068 5.997
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/notameViz.Rcheck/00check.log’
for details.
notameViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL notameViz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-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) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 [2025-11-10 02:02:28] Saved to: /tmp/RtmpOMKILt\test\recursive/file26e29e2669061e.pdf
INFO [2025-11-10 02:02:28] Saved to: /tmp/RtmpOMKILt/file26e29e2ea04a87.pdf
INFO [2025-11-10 02:02:29] Saved to: /tmp/RtmpOMKILt/file26e29e22ff9825.emf
INFO [2025-11-10 02:02:29] Saved to: /tmp/RtmpOMKILt/file26e29e28a38007.svg
INFO [2025-11-10 02:02:29] Saved to: /tmp/RtmpOMKILt/file26e29e7226c58f.png
INFO [2025-11-10 02:02:29] Saved to: /tmp/RtmpOMKILt/file26e29e213ca28e.tiff
INFO [2025-11-10 02:02:30] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-10 02:02:30] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-10 02:02:31] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-10 02:02:31] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-10 02:02:31] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-10 02:02:31] Saved line plots with mean line to: /tmp/RtmpOMKILt\test\
INFO [2025-11-10 02:02:32] Saved to: /tmp/RtmpOMKILt\test\/Glucose.emf
INFO [2025-11-10 02:02:32] Saved to: /tmp/RtmpOMKILt\test\/Threoline.emf
INFO [2025-11-10 02:02:32] Saved to: /tmp/RtmpOMKILt\test\/5-AVAB.emf
INFO [2025-11-10 02:02:32] Saved to: /tmp/RtmpOMKILt\test\/1_2 acid.emf
INFO [2025-11-10 02:02:33] Saved to: /tmp/RtmpOMKILt\test\/20_0 carbon chain.emf
INFO [2025-11-10 02:02:33] Saved line plots with mean line to: /tmp/RtmpOMKILt\test\
INFO [2025-11-10 02:02:33] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-10 02:02:34] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-10 02:02:34] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-10 02:02:34] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-10 02:02:34] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-10 02:02:34] Saved group boxplots to: /tmp/RtmpOMKILt\test\
INFO [2025-11-10 02:02:35] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-10 02:02:35] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-10 02:02:35] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-10 02:02:36] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-10 02:02:36] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-10 02:02:36] Saved group boxplots to: /tmp/RtmpOMKILt\test\
INFO [2025-11-10 02:02:36] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-10 02:02:37] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-10 02:02:37] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-10 02:02:37] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-10 02:02:37] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-10 02:02:37] Saved beeswarm plots to: /tmp/RtmpOMKILt\test\
INFO [2025-11-10 02:02:38] Saved to: /tmp/RtmpOMKILt\test\/Glucose.emf
INFO [2025-11-10 02:02:38] Saved to: /tmp/RtmpOMKILt\test\/Threoline.emf
INFO [2025-11-10 02:02:38] Saved to: /tmp/RtmpOMKILt\test\/5-AVAB.emf
INFO [2025-11-10 02:02:39] Saved to: /tmp/RtmpOMKILt\test\/1_2 acid.emf
INFO [2025-11-10 02:02:39] Saved to: /tmp/RtmpOMKILt\test\/20_0 carbon chain.emf
INFO [2025-11-10 02:02:39] Saved beeswarm plots to: /tmp/RtmpOMKILt\test\
INFO [2025-11-10 02:02:39] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-10 02:02:39] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-10 02:02:40] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-10 02:02:40] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-10 02:02:40] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-10 02:02:40] Saved scatter plots to: /tmp/RtmpOMKILt\test\
INFO [2025-11-10 02:02:41] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-10 02:02:41] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-10 02:02:41] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-10 02:02:41] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-10 02:02:42] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-10 02:02:42] Saved scatter plots to: /tmp/RtmpOMKILt\test\
INFO [2025-11-10 02:02:42] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-10 02:02:43] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-10 02:02:43] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-10 02:02:44] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-10 02:02:44] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-10 02:02:44] Saved line plots with mean line to: /tmp/RtmpOMKILt\test\
INFO [2025-11-10 02:02:45] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_259_9623a4_4322.emf
INFO [2025-11-10 02:02:45] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_108_1065a2_6121.emf
INFO [2025-11-10 02:02:46] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_158_23a1_4128.emf
INFO [2025-11-10 02:02:46] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_251_0056a0_6161.emf
INFO [2025-11-10 02:02:46] Saved to: /tmp/RtmpOMKILt\test\/HILIC_neg_401_52a4_211.emf
INFO [2025-11-10 02:02:46] Saved line plots with mean line to: /tmp/RtmpOMKILt\test\
INFO [2025-11-10 02:02:47]
Saved batch plots to: /tmp/RtmpOMKILt\test\batch_plots.pdf
INFO [2025-11-10 02:02:47] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-10 02:02:48] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-10 02:02:48] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-10 02:02:48]
92% of features flagged for low quality
INFO [2025-11-10 02:02:48] Identified m/z column Average_Mz and retention time column Average_Rt_min
INFO [2025-11-10 02:02:48] 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
27.678 0.957 28.631
notameViz.Rcheck/notameViz-Ex.timings
| name | user | system | elapsed | |
| manhattan_plot | 6.447 | 1.542 | 4.829 | |
| mz_rt_plot | 4.777 | 1.862 | 3.124 | |
| plot_dendrogram | 0.514 | 0.029 | 0.543 | |
| plot_dist_density | 1.509 | 0.555 | 1.491 | |
| plot_effect_heatmap | 4.975 | 1.539 | 3.239 | |
| plot_injection_lm | 11.406 | 5.047 | 5.224 | |
| plot_p_histogram | 3.535 | 1.416 | 1.704 | |
| plot_pca | 0.41 | 0.16 | 0.57 | |
| plot_pca_arrows | 0.865 | 0.145 | 1.011 | |
| plot_pca_hexbin | 0.218 | 0.004 | 0.222 | |
| plot_pca_loadings | 0.313 | 0.035 | 0.348 | |
| plot_quality | 1.447 | 0.063 | 1.511 | |
| plot_sample_boxplots | 1.091 | 0.050 | 1.142 | |
| plot_sample_heatmap | 0.640 | 0.014 | 0.654 | |
| plot_tsne | 0.456 | 0.027 | 0.483 | |
| plot_tsne_arrows | 0.829 | 0.024 | 0.853 | |
| plot_tsne_hexbin | 0.274 | 0.002 | 0.276 | |
| save_QC_plots | 11.572 | 2.532 | 10.606 | |
| save_batch_plots | 9.134 | 0.116 | 9.252 | |
| save_beeswarm_plots | 5.942 | 0.068 | 5.997 | |
| save_dc_plots | 2.774 | 0.585 | 2.790 | |
| save_group_boxplots | 7.876 | 0.185 | 8.065 | |
| save_group_lineplots | 7.702 | 0.090 | 7.792 | |
| save_plot | 0.793 | 0.043 | 0.836 | |
| save_scatter_plots | 3.391 | 0.012 | 3.404 | |
| save_subject_line_plots | 3.762 | 0.242 | 4.005 | |
| visualize_clusters | 2.015 | 0.009 | 2.024 | |
| volcano_plot | 3.245 | 1.343 | 1.478 | |