Mac ARM64 build report for BioC 3.19 - CHECK results for SWATH2stats on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4461
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*

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### Running command:
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###   /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_1.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/SWATH2stats.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SWATH2stats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SWATH2stats’ version ‘1.34.0’
* 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-3.19-bioc-mac-arm64/meat/SWATH2stats.Rcheck/00check.log’
for details.

Installation output

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


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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

name	user	system	elapsed
JPP_update	0.042	0.001	0.043
add_genesymbol	0.002	0.000	0.003
assess_decoy_rate	0.04	0.00	0.04
assess_fdr_byrun	0.058	0.004	0.062
assess_fdr_overall	0.058	0.004	0.063
convert4MSstats	0.235	0.004	0.239
convert4PECA	0.057	0.001	0.058
convert4aLFQ	0.256	0.005	0.261
convert4mapDIA	0.304	0.007	0.311
convert4pythonscript	0.047	0.002	0.049
convert_protein_ids	0	0	0
count_analytes	0.042	0.002	0.045
disaggregate	0.076	0.006	0.081
filter_all_peptides	0.046	0.002	0.047
filter_mscore	0.058	0.002	0.059
filter_mscore_condition	0.056	0.002	0.060
filter_mscore_fdr	0.117	0.005	0.124
filter_mscore_freqobs	0.058	0.003	0.062
filter_on_max_peptides	0.052	0.002	0.054
filter_on_min_peptides	0.052	0.002	0.054
filter_proteotypic_peptides	0.049	0.002	0.051
import_data	0.199	0.004	0.203
load_mart	0.370	0.031	3.617
mscore4assayfdr	0.099	0.001	0.099
mscore4pepfdr	0.112	0.008	0.120
mscore4protfdr	0.074	0.005	0.079
plot.fdr_cube	0.054	0.003	0.057
plot.fdr_table	0.065	0.004	0.069
plot_correlation_between_samples	0.145	0.004	0.149
plot_variation	0.130	0.009	0.139
plot_variation_vs_total	0.301	0.004	0.306
reduce_OpenSWATH_output	0.043	0.001	0.044
removeDecoyProteins	0.041	0.001	0.042
sample_annotation	0.046	0.003	0.049
transform_MSstats_OpenSWATH	0.001	0.000	0.001
unifyProteinGroupLabels	0.040	0.001	0.041
validate_columns	0	0	0
write_matrix_peptides	0.040	0.001	0.041
write_matrix_proteins	0.045	0.002	0.047

CHECK results for SWATH2stats on kjohnson3

Summary

Command output

Installation output

Tests output

Example timings