Ossama Edbali
| Snapshot Date: 2026-05-21 13:40 -0400 (Thu, 21 May 2026) |
| git_url: https://git.bioconductor.org/packages/lcmsPlot |
| git_branch: RELEASE_3_23 |
| git_last_commit: 146cffe |
| git_last_commit_date: 2026-04-28 09:06:23 -0400 (Tue, 28 Apr 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-22 11:33 -0400 (Fri, 22 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4995 |
| 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 1155/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| lcmsPlot 1.0.0 (landing page) Ossama Edbali
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for lcmsPlot in R Universe. | ||||||||||||||
|
To the developers/maintainers of the lcmsPlot package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/lcmsPlot.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: lcmsPlot |
| Version: 1.0.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:lcmsPlot.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings lcmsPlot_1.0.0.tar.gz |
| StartedAt: 2026-05-22 02:47:18 -0400 (Fri, 22 May 2026) |
| EndedAt: 2026-05-22 02:55:33 -0400 (Fri, 22 May 2026) |
| EllapsedTime: 494.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: lcmsPlot.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:lcmsPlot.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings lcmsPlot_1.0.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/lcmsPlot.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-22 06:47:19 UTC
* checking for file ‘lcmsPlot/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lcmsPlot’ 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 ‘lcmsPlot’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* 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
get_XCMSnExp_object_example 23.455 3.789 17.126
lp_peak_density 17.182 5.375 12.488
lp_rt_diff_plot 16.242 5.716 12.200
XcmsRawList 17.185 1.145 18.334
lp_total_ion_current 13.825 4.125 9.319
lp_layout 9.151 1.742 10.757
iterate_plot_batches 8.406 1.125 9.531
lp_rt_line 5.404 0.534 5.941
lp_grid 5.195 0.352 5.547
lp_mass_trace 4.900 0.342 5.257
* 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: OK
lcmsPlot.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL lcmsPlot ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘lcmsPlot’ ... ** this is package ‘lcmsPlot’ version ‘1.0.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘create_chromatograms’ with signature ‘"DBIConnection","data.frame","list","NULL"’: no definition for class “DBIConnection” in method for ‘create_chromatograms’ with signature ‘"MChromatograms","data.frame","list","NULL"’: no definition for class “MChromatograms” in method for ‘create_chromatograms’ with signature ‘"XChromatogram","data.frame","list","NULL"’: no definition for class “XChromatogram” in method for ‘create_chromatograms’ with signature ‘"XChromatograms","data.frame","list","NULL"’: no definition for class “XChromatograms” ** 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 (lcmsPlot)
lcmsPlot.Rcheck/tests/testthat.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(lcmsPlot)
>
> test_check("lcmsPlot")
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
This is xcms version 4.10.0
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 635 regions of interest ... OK: 300 found.
This is xcms version 4.10.0
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 694 regions of interest ... OK: 312 found.
Sample number 1 used as center sample.
Aligning wt15.CDF against ko15.CDF ... OK
Applying retention time adjustment to the identified chromatographic peaks ... OK
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
This is xcms version 4.10.0
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 635 regions of interest ... OK: 300 found.
This is xcms version 4.10.0
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 694 regions of interest ... OK: 312 found.
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method.
This is xcms version 4.10.0
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 635 regions of interest ... OK: 300 found.
This is xcms version 4.10.0
Detecting mass traces at 25 ppm ... OK
Detecting chromatographic peaks in 694 regions of interest ... OK: 312 found.
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 107 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 107 ]
>
> proc.time()
user system elapsed
66.716 13.043 65.206
lcmsPlot.Rcheck/lcmsPlot-Ex.timings
| name | user | system | elapsed | |
| MZmineFeatureListsSource | 0.025 | 0.006 | 0.031 | |
| MsDialPeaksSource | 0.011 | 0.001 | 0.012 | |
| XcmsRawList | 17.185 | 1.145 | 18.334 | |
| create_data_container_from_obj | 0.010 | 0.002 | 0.012 | |
| create_xcms_raw_list | 3.786 | 0.731 | 4.520 | |
| get_XCMSnExp_object_example | 23.455 | 3.789 | 17.126 | |
| iterate_plot_batches | 8.406 | 1.125 | 9.531 | |
| lcmsPlot | 0.008 | 0.000 | 0.009 | |
| lp_arrange | 2.336 | 0.170 | 2.507 | |
| lp_chromatogram | 3.252 | 0.252 | 3.505 | |
| lp_compound_discoverer | 0.000 | 0.000 | 0.001 | |
| lp_facets | 2.747 | 0.149 | 2.897 | |
| lp_get_plot | 4.517 | 0.285 | 4.803 | |
| lp_grid | 5.195 | 0.352 | 5.547 | |
| lp_intensity_map | 4.109 | 0.574 | 4.683 | |
| lp_labels | 2.339 | 0.171 | 2.510 | |
| lp_layout | 9.151 | 1.742 | 10.757 | |
| lp_legend | 2.248 | 0.116 | 2.364 | |
| lp_mass_trace | 4.900 | 0.342 | 5.257 | |
| lp_peak_density | 17.182 | 5.375 | 12.488 | |
| lp_rt_diff_plot | 16.242 | 5.716 | 12.200 | |
| lp_rt_line | 5.404 | 0.534 | 5.941 | |
| lp_spectra | 1.713 | 0.150 | 1.863 | |
| lp_total_ion_current | 13.825 | 4.125 | 9.319 | |
| next_plot | 3.726 | 0.552 | 4.279 | |
| plus-lcmsPlotClass-function-method | 2.689 | 0.534 | 3.223 | |
| show-ExternalDataSource-method | 0.002 | 0.000 | 0.003 | |
| show-lcmsPlotClass-method | 1.991 | 0.146 | 2.138 | |
| show-lcmsPlotDataContainer-method | 0.005 | 0.000 | 0.006 | |