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This page was generated on 2023-10-20 09:38:13 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 2051/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SWATH2stats 1.30.1  (landing page)
Peter Blattmann
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/SWATH2stats
git_branch: RELEASE_3_17
git_last_commit: b49bb00
git_last_commit_date: 2023-07-01 10:54:28 -0400 (Sat, 01 Jul 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    ERROR    OK  

CHECK results for SWATH2stats on kjohnson2


To the developers/maintainers of the SWATH2stats package:
- 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: 1.30.1
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_1.30.1.tar.gz
StartedAt: 2023-10-19 05:41:39 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 05:47:59 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 380.8 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_1.30.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SWATH2stats.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SWATH2stats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SWATH2stats’ version ‘1.30.1’
* 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 R 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 ... NOTE
checkRd: (-1) sample_annotation.Rd:29: Escaped LaTeX specials: \_
* 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
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
load_mart 0.722  0.083  11.201
* 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 in ‘inst/doc’ ... 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SWATH2stats.Rcheck/00check.log’
for details.


Installation output

SWATH2stats.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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_update0.1350.0070.261
add_genesymbol0.0070.0010.016
assess_decoy_rate0.1260.0050.238
assess_fdr_byrun0.2090.0100.388
assess_fdr_overall0.1780.0100.347
convert4MSstats0.6220.0151.135
convert4PECA0.1940.0050.356
convert4aLFQ0.6450.0161.178
convert4mapDIA0.4130.0120.760
convert4pythonscript0.1740.0060.321
convert_protein_ids000
count_analytes0.1540.0040.280
disaggregate0.2550.0090.478
filter_all_peptides0.1720.0060.321
filter_mscore0.1930.0060.362
filter_mscore_condition0.2010.0080.361
filter_mscore_fdr0.4130.0110.766
filter_mscore_freqobs0.1960.0040.356
filter_on_max_peptides0.1850.0040.335
filter_on_min_peptides0.1820.0040.343
filter_proteotypic_peptides0.1750.0050.307
import_data0.5110.0230.949
load_mart 0.722 0.08311.201
mscore4assayfdr0.3480.0090.636
mscore4pepfdr0.3180.0070.586
mscore4protfdr0.2830.0050.514
plot.fdr_cube0.2100.0090.402
plot.fdr_table0.1760.0060.324
plot_correlation_between_samples0.5020.0140.923
plot_variation0.4920.0190.919
plot_variation_vs_total0.4610.0150.871
reduce_OpenSWATH_output0.1460.0030.269
removeDecoyProteins0.1520.0050.278
sample_annotation0.2080.0070.397
transform_MSstats_OpenSWATH0.0030.0000.008
unifyProteinGroupLabels0.1540.0030.294
validate_columns0.0010.0010.002
write_matrix_peptides0.1580.0040.293
write_matrix_proteins0.1760.0050.329