Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-08-02 12:05 -0400 (Sat, 02 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4535
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 2117/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SWATH2stats 1.39.0  (landing page)
Peter Blattmann
Snapshot Date: 2025-08-01 13:25 -0400 (Fri, 01 Aug 2025)
git_url: https://git.bioconductor.org/packages/SWATH2stats
git_branch: devel
git_last_commit: 00d180f
git_last_commit_date: 2025-04-15 10:55:50 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for SWATH2stats on nebbiolo2

To the developers/maintainers of the SWATH2stats package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SWATH2stats.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.

raw results


Summary

Package: SWATH2stats
Version: 1.39.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SWATH2stats_1.39.0.tar.gz
StartedAt: 2025-08-02 03:26:59 -0400 (Sat, 02 Aug 2025)
EndedAt: 2025-08-02 03:29:50 -0400 (Sat, 02 Aug 2025)
EllapsedTime: 171.2 seconds
RetCode: 0
Status:   OK  
CheckDir: SWATH2stats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SWATH2stats_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SWATH2stats.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SWATH2stats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SWATH2stats’ version ‘1.39.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package which this enhances but not available for checking: ‘aLFQ’
* 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 ‘SWATH2stats’ 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 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
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
load_mart 1.548  0.279   5.168
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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


Installation output

SWATH2stats.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SWATH2stats
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SWATH2stats’ ...
** this is package ‘SWATH2stats’ version ‘1.39.0’
** 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 (SWATH2stats)

Tests output

SWATH2stats.Rcheck/tests/test-all.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
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)
> test_check("SWATH2stats")
Loading required package: SWATH2stats
[1] "peterb_J131223_054"
[1] "peterb_L150425_011_SW"
[1] "peterb_L150514_002_SW"
[ FAIL 0 | WARN 74 | SKIP 0 | PASS 113 ]

[ FAIL 0 | WARN 74 | SKIP 0 | PASS 113 ]
> 
> proc.time()
   user  system elapsed 
 12.391   1.098  16.458 

Example timings

SWATH2stats.Rcheck/SWATH2stats-Ex.timings

nameusersystemelapsed
JPP_update0.1070.0060.113
add_genesymbol0.0060.0000.006
assess_decoy_rate0.1230.0000.122
assess_fdr_byrun0.1740.0010.175
assess_fdr_overall0.2910.0010.293
convert4MSstats0.6650.0920.756
convert4PECA0.1550.0050.160
convert4aLFQ0.6640.0030.667
convert4mapDIA0.3470.0000.347
convert4pythonscript0.1240.0000.123
convert_protein_ids000
count_analytes0.1250.0000.126
disaggregate0.6360.0450.681
filter_all_peptides0.1160.0030.119
filter_mscore0.1660.0130.165
filter_mscore_condition0.1510.0010.139
filter_mscore_fdr0.3090.0000.309
filter_mscore_freqobs0.1670.0010.151
filter_on_max_peptides0.1470.0010.134
filter_on_min_peptides0.1600.0010.142
filter_proteotypic_peptides0.1190.0010.113
import_data0.4660.0150.481
load_mart1.5480.2795.168
mscore4assayfdr0.2230.0530.277
mscore4pepfdr0.2010.0040.205
mscore4protfdr0.1670.0010.169
plot.fdr_cube0.1310.0040.135
plot.fdr_table0.1230.0020.126
plot_correlation_between_samples0.3940.0200.414
plot_variation0.3920.0390.431
plot_variation_vs_total0.3330.0230.355
reduce_OpenSWATH_output0.1000.0000.099
removeDecoyProteins0.1000.0010.102
sample_annotation0.1200.0020.123
transform_MSstats_OpenSWATH0.0030.0000.002
unifyProteinGroupLabels0.1030.0030.106
validate_columns0.0000.0000.001
write_matrix_peptides0.1160.0010.117
write_matrix_proteins0.1050.0000.105