Sarah Szvetecz
| Snapshot Date: 2026-04-23 13:40 -0400 (Thu, 23 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/MSstatsResponse |
| git_branch: devel |
| git_last_commit: 3632573 |
| git_last_commit_date: 2026-04-23 13:05:45 -0400 (Thu, 23 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-24 11:36 -0400 (Fri, 24 Apr 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" | 4958 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4705 |
| 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 1428/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MSstatsResponse 1.1.2 (landing page) Sarah Szvetecz
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| See other builds for MSstatsResponse in R Universe. | ||||||||||||||
|
To the developers/maintainers of the MSstatsResponse package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsResponse.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: MSstatsResponse |
| Version: 1.1.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsResponse.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsResponse_1.1.2.tar.gz |
| StartedAt: 2026-04-23 20:59:42 -0400 (Thu, 23 Apr 2026) |
| EndedAt: 2026-04-23 21:00:28 -0400 (Thu, 23 Apr 2026) |
| EllapsedTime: 45.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MSstatsResponse.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MSstatsResponse.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MSstatsResponse_1.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/MSstatsResponse.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-24 00:59:43 UTC
* using option ‘--no-vignettes’
* checking for file ‘MSstatsResponse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsResponse’ version ‘1.1.2’
* 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 ‘MSstatsResponse’ can be installed ... OK
* checking installed package size ... INFO
installed size is 7.8Mb
sub-directories of 1Mb or more:
data 3.7Mb
extdata 3.9Mb
* 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 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 ... NOTE
.build_concentration_ladders: no visible global function definition for
‘median’
.extractTemplatesFromData : .getMeanProfile: no visible binding for
global variable ‘dose_str’
.make_tpr_panel: no visible global function definition for ‘setNames’
calculatePeptideWeights: no visible binding for global variable ‘n_obs’
calculatePeptideWeights: no visible global function definition for
‘median’
calculatePeptideWeights: no visible binding for global variable
‘peptide_median_light’
calculatePeptideWeights: no visible binding for global variable
‘peptide_rank’
calculatePeptideWeights: no visible binding for global variable
‘monotonicity_score’
calculatePeptideWeights: no visible binding for global variable
‘coverage_score’
calculatePeptideWeights: no visible binding for global variable
‘light_intensity_score’
calculatePeptideWeights: no visible binding for global variable
‘validity_flag’
calculateTurnoverRatios: no visible binding for global variable
‘TimeVal’
calculateTurnoverRatios: no visible binding for global variable ‘Label’
calculateTurnoverRatios: no visible binding for global variable
‘Protein’
calculateTurnoverRatios: no visible binding for global variable
‘BaseSequence’
calculateTurnoverRatios: no visible binding for global variable ‘Run’
calculateTurnoverRatios: no visible binding for global variable ‘Heavy’
calculateTurnoverRatios: no visible binding for global variable ‘Light’
calculateTurnoverRatios: no visible binding for global variable ‘Total’
calculateTurnoverRatios: no visible binding for global variable
‘H_frac’
calculateTurnoverRatios: no visible binding for global variable
‘tracer_factor’
plotHitRateMSstatsResponse: no visible binding for global variable
‘Protein’
plotIsotonic: no visible binding for global variable ‘weight’
Undefined global functions or variables:
BaseSequence H_frac Heavy Label Light Protein Run TimeVal Total
coverage_score dose_str light_intensity_score median
monotonicity_score n_obs peptide_median_light peptide_rank setNames
tracer_factor validity_flag weight
Consider adding
importFrom("stats", "median", "setNames")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in Rd file 'PredictIC50.Rd'
‘weights’
Undocumented arguments in Rd file 'bootstrapIC50.Rd'
‘weights’
Undocumented arguments in Rd file 'bootstrapIC50LogScale.Rd'
‘weights’
Undocumented arguments in Rd file 'bootstrapIC50Precalculated.Rd'
‘weights’
Undocumented arguments in Rd file 'plot_tpr_power_curve.Rd'
‘simulation_results’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/MSstatsResponse.Rcheck/00check.log’
for details.
MSstatsResponse.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MSstatsResponse ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘MSstatsResponse’ ... ** this is package ‘MSstatsResponse’ version ‘1.1.2’ ** using staged installation ** R ** data ** 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 (MSstatsResponse)
MSstatsResponse.Rcheck/tests/testthat.Rout
R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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(MSstatsResponse)
>
> test_check("MSstatsResponse")
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 200 ]
>
> proc.time()
user system elapsed
11.414 1.241 12.314
MSstatsResponse.Rcheck/MSstatsResponse-Ex.timings
| name | user | system | elapsed | |
| DIA_MSstats_Normalized | 1.194 | 0.222 | 1.445 | |
| MSstatsPrepareDoseResponseFit | 0.280 | 0.008 | 0.296 | |
| PredictIC50 | 0.813 | 0.174 | 0.878 | |
| calculatePeptideWeights | 0 | 0 | 0 | |
| calculateTurnoverRatios | 0 | 0 | 0 | |
| convertGroupToNumericDose | 0.001 | 0.001 | 0.002 | |
| doseResponseFit | 0.276 | 0.018 | 0.298 | |
| futureExperimentSimulation | 0.146 | 0.014 | 0.163 | |
| parse_timepoint | 0.002 | 0.000 | 0.002 | |
| plot_tpr_power_curve | 0.000 | 0.001 | 0.000 | |
| predictIC50Parallel | 0.264 | 0.010 | 1.491 | |
| run_tpr_simulation | 0.000 | 0.000 | 0.001 | |
| visualizeResponseProtein | 0.667 | 0.009 | 0.689 | |