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This page was generated on 2024-12-24 11:42 -0500 (Tue, 24 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" 4373
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: 2024-12-23 13:40 -0500 (Mon, 23 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 palomino7

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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SWATH2stats.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SWATH2stats_1.37.0.tar.gz
StartedAt: 2024-12-24 05:35:29 -0500 (Tue, 24 Dec 2024)
EndedAt: 2024-12-24 05:38:17 -0500 (Tue, 24 Dec 2024)
EllapsedTime: 168.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SWATH2stats.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SWATH2stats.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings SWATH2stats_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/SWATH2stats.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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'
 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:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL SWATH2stats
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  16.15    1.14   19.01 

Example timings

SWATH2stats.Rcheck/SWATH2stats-Ex.timings

nameusersystemelapsed
JPP_update0.100.010.12
add_genesymbol0.020.000.01
assess_decoy_rate0.140.000.14
assess_fdr_byrun0.200.020.22
assess_fdr_overall0.270.000.27
convert4MSstats0.620.030.66
convert4PECA0.140.020.15
convert4aLFQ0.630.010.64
convert4mapDIA0.570.030.61
convert4pythonscript0.180.000.17
convert_protein_ids000
count_analytes0.140.000.14
disaggregate0.560.000.57
filter_all_peptides0.090.020.11
filter_mscore0.170.000.17
filter_mscore_condition0.150.000.14
filter_mscore_fdr0.390.000.39
filter_mscore_freqobs0.170.020.19
filter_on_max_peptides0.150.000.15
filter_on_min_peptides0.180.000.17
filter_proteotypic_peptides0.170.000.18
import_data0.480.010.50
load_mart1.830.314.39
mscore4assayfdr0.300.030.33
mscore4pepfdr0.280.000.28
mscore4protfdr0.310.050.36
plot.fdr_cube0.240.020.25
plot.fdr_table0.20.00.2
plot_correlation_between_samples0.510.010.53
plot_variation0.580.020.59
plot_variation_vs_total0.460.000.46
reduce_OpenSWATH_output0.140.000.14
removeDecoyProteins0.110.000.11
sample_annotation0.110.050.16
transform_MSstats_OpenSWATH000
unifyProteinGroupLabels0.130.000.12
validate_columns000
write_matrix_peptides0.120.000.13
write_matrix_proteins0.110.000.11