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This page was generated on 2024-06-18 17:58 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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 2113/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SWATH2stats 1.34.0  (landing page)
Peter Blattmann
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/SWATH2stats
git_branch: RELEASE_3_19
git_last_commit: 4ba3d06
git_last_commit_date: 2024-04-30 10:46:14 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 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 nebbiolo1

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: 1.34.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SWATH2stats_1.34.0.tar.gz
StartedAt: 2024-06-17 04:28:27 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 04:31:20 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 172.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SWATH2stats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SWATH2stats_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SWATH2stats.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 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
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.


Installation output

SWATH2stats.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SWATH2stats
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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 
 12.790   0.768  16.460 

Example timings

SWATH2stats.Rcheck/SWATH2stats-Ex.timings

nameusersystemelapsed
JPP_update0.1000.0080.108
add_genesymbol0.0070.0000.006
assess_decoy_rate0.1010.0040.105
assess_fdr_byrun0.1620.0360.198
assess_fdr_overall0.1380.0200.158
convert4MSstats0.5710.0640.635
convert4PECA0.1460.0000.146
convert4aLFQ0.5580.0080.566
convert4mapDIA0.3340.0160.350
convert4pythonscript0.1140.0040.118
convert_protein_ids0.0010.0000.000
count_analytes0.1310.0000.131
disaggregate0.1880.0000.189
filter_all_peptides0.1260.0000.126
filter_mscore0.1730.0040.161
filter_mscore_condition0.1750.0000.162
filter_mscore_fdr0.3040.0000.304
filter_mscore_freqobs0.1470.0040.139
filter_on_max_peptides0.1690.0160.171
filter_on_min_peptides0.1500.0040.141
filter_proteotypic_peptides0.1220.0000.122
import_data0.4350.0160.451
load_mart1.0980.2234.977
mscore4assayfdr0.2990.0240.323
mscore4pepfdr0.2370.0000.237
mscore4protfdr0.2010.0160.216
plot.fdr_cube0.1440.0000.143
plot.fdr_table0.1590.0000.158
plot_correlation_between_samples0.4260.0400.465
plot_variation0.4190.0040.423
plot_variation_vs_total0.3380.0080.347
reduce_OpenSWATH_output0.1290.0000.129
removeDecoyProteins0.1170.0040.121
sample_annotation0.1470.0000.148
transform_MSstats_OpenSWATH0.0030.0000.003
unifyProteinGroupLabels0.1460.0080.153
validate_columns0.0000.0010.001
write_matrix_peptides0.1150.0030.119
write_matrix_proteins0.1130.0040.117