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This page was generated on 2024-12-23 11:44 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 2082/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SWATH2stats 1.37.0  (landing page)
Peter Blattmann
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/SWATH2stats
git_branch: devel
git_last_commit: 8dd5551
git_last_commit_date: 2024-10-29 10:04:27 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for SWATH2stats on lconway

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: 1.37.0
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_1.37.0.tar.gz
StartedAt: 2024-12-22 23:40:04 -0500 (Sun, 22 Dec 2024)
EndedAt: 2024-12-22 23:42:58 -0500 (Sun, 22 Dec 2024)
EllapsedTime: 173.7 seconds
RetCode: 0
Status:   OK  
CheckDir: SWATH2stats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SWATH2stats.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SWATH2stats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SWATH2stats’ version ‘1.37.0’
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
load_mart 1.317  0.128   8.032
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


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/4.5-x86_64/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


R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 0 | WARN 74 | SKIP 0 | PASS 113 ]

[ FAIL 0 | WARN 74 | SKIP 0 | PASS 113 ]
> 
> proc.time()
   user  system elapsed 
 14.463   0.800  18.734 

Example timings

SWATH2stats.Rcheck/SWATH2stats-Ex.timings

nameusersystemelapsed
JPP_update0.1320.0040.138
add_genesymbol0.0060.0000.006
assess_decoy_rate0.1230.0020.127
assess_fdr_byrun0.1830.0110.199
assess_fdr_overall0.2880.0100.300
convert4MSstats0.9120.0170.934
convert4PECA0.1590.0060.167
convert4aLFQ0.6010.0210.624
convert4mapDIA0.3870.0170.408
convert4pythonscript0.1290.0040.132
convert_protein_ids0.0000.0000.001
count_analytes0.1490.0070.155
disaggregate0.2370.0140.254
filter_all_peptides0.1320.0040.138
filter_mscore0.1950.0110.207
filter_mscore_condition0.1730.0070.181
filter_mscore_fdr0.3640.0190.386
filter_mscore_freqobs0.1690.0050.175
filter_on_max_peptides0.1580.0040.165
filter_on_min_peptides0.1790.0050.188
filter_proteotypic_peptides0.1370.0030.142
import_data0.4540.0170.475
load_mart1.3170.1288.032
mscore4assayfdr0.3000.0210.323
mscore4pepfdr0.3330.0160.352
mscore4protfdr0.2420.0050.249
plot.fdr_cube0.1630.0070.172
plot.fdr_table0.1500.0070.159
plot_correlation_between_samples0.5050.0110.520
plot_variation0.4770.0140.495
plot_variation_vs_total0.3770.0050.383
reduce_OpenSWATH_output0.1310.0030.135
removeDecoyProteins0.1440.0050.149
sample_annotation0.1490.0070.156
transform_MSstats_OpenSWATH0.0020.0010.004
unifyProteinGroupLabels0.1220.0030.126
validate_columns0.0000.0000.001
write_matrix_peptides0.1530.0030.157
write_matrix_proteins0.1310.0030.134