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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 2098/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SWATH2stats 1.36.0  (landing page)
Peter Blattmann
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/SWATH2stats
git_branch: RELEASE_3_20
git_last_commit: 0378c99
git_last_commit_date: 2024-10-29 10:04:27 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for SWATH2stats on kjohnson1

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: 1.36.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SWATH2stats_1.36.0.tar.gz
StartedAt: 2024-12-21 11:24:42 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 11:27:22 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 159.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: SWATH2stats.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SWATH2stats_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SWATH2stats.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SWATH2stats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SWATH2stats’ version ‘1.36.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  [1] "peterb_J131223_054"
  [1] "peterb_L150425_011_SW"
  [1] "peterb_L150514_002_SW"
  [ FAIL 1 | WARN 74 | SKIP 0 | PASS 112 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_plots.R:85:3'): variation plot vs total ──────────────────────
  cv.val1.total == as.numeric(test1.total[, "cv"]) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 74 | SKIP 0 | PASS 112 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.


Installation output

SWATH2stats.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SWATH2stats
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘SWATH2stats’ ...
** 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.fail


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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)
> test_check("SWATH2stats")
Loading required package: SWATH2stats
[1] "peterb_J131223_054"
[1] "peterb_L150425_011_SW"
[1] "peterb_L150514_002_SW"
[ FAIL 1 | WARN 74 | SKIP 0 | PASS 112 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plots.R:85:3'): variation plot vs total ──────────────────────
cv.val1.total == as.numeric(test1.total[, "cv"]) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 1 | WARN 74 | SKIP 0 | PASS 112 ]
Error: Test failures
Execution halted

Example timings

SWATH2stats.Rcheck/SWATH2stats-Ex.timings

nameusersystemelapsed
JPP_update0.0820.0030.095
add_genesymbol0.0040.0000.005
assess_decoy_rate0.1020.0040.122
assess_fdr_byrun0.1780.0080.195
assess_fdr_overall0.2920.0080.310
convert4MSstats0.7680.0140.793
convert4PECA0.1860.0030.190
convert4aLFQ0.7530.0180.772
convert4mapDIA0.8860.0190.911
convert4pythonscript0.1680.0040.172
convert_protein_ids0.0000.0000.001
count_analytes0.1520.0040.156
disaggregate0.2540.0130.269
filter_all_peptides0.1630.0020.165
filter_mscore0.2410.0090.219
filter_mscore_condition0.3610.0240.207
filter_mscore_fdr0.5620.0360.432
filter_mscore_freqobs0.2260.0080.199
filter_on_max_peptides0.2930.0170.192
filter_on_min_peptides0.2570.0170.230
filter_proteotypic_peptides0.2090.0090.162
import_data0.6600.0150.683
load_mart1.1920.1031.930
mscore4assayfdr0.3190.0150.336
mscore4pepfdr0.3000.0130.314
mscore4protfdr0.2580.0080.267
plot.fdr_cube0.1810.0060.188
plot.fdr_table0.1810.0070.189
plot_correlation_between_samples0.5210.0110.534
plot_variation0.4760.0070.485
plot_variation_vs_total0.3940.0060.403
reduce_OpenSWATH_output0.1590.0040.164
removeDecoyProteins0.1630.0040.168
sample_annotation0.2180.0080.226
transform_MSstats_OpenSWATH0.0040.0000.004
unifyProteinGroupLabels0.1730.0030.175
validate_columns0.0010.0010.002
write_matrix_peptides0.1770.0030.181
write_matrix_proteins0.1610.0030.165