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This page was generated on 2021-10-15 15:06:55 -0400 (Fri, 15 Oct 2021).

CHECK results for SWATH2stats on machv2

To the developers/maintainers of the SWATH2stats package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1877/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SWATH2stats 1.22.0  (landing page)
Peter Blattmann
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/SWATH2stats
git_branch: RELEASE_3_13
git_last_commit: 9dd20d3
git_last_commit_date: 2021-05-19 12:16:16 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SWATH2stats
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SWATH2stats_1.22.0.tar.gz
StartedAt: 2021-10-15 00:32:43 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 00:36:03 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 200.0 seconds
RetCode: 0
Status:   OK  
CheckDir: SWATH2stats.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SWATH2stats.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SWATH2stats_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/SWATH2stats.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SWATH2stats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SWATH2stats’ version ‘1.22.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 ... 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 4.992  0.111   8.539
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.



Installation output

SWATH2stats.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0 | WARN 73 | SKIP 0 | PASS 113 ]
> 
> proc.time()
   user  system elapsed 
 21.151   0.702  25.802 

Example timings

SWATH2stats.Rcheck/SWATH2stats-Ex.timings

nameusersystemelapsed
JPP_update0.1670.0040.172
add_genesymbol0.0110.0010.012
assess_decoy_rate0.1450.0030.149
assess_fdr_byrun0.5230.0090.532
assess_fdr_overall0.2160.0130.230
convert4MSstats0.6120.0130.625
convert4PECA0.1500.0030.153
convert4aLFQ0.7520.0180.770
convert4mapDIA0.5500.0140.565
convert4pythonscript0.1900.0040.195
convert_protein_ids000
count_analytes0.1860.0060.192
disaggregate0.3450.0170.362
filter_all_peptides0.2010.0040.205
filter_mscore0.2330.0100.243
filter_mscore_condition0.1730.0080.180
filter_mscore_fdr0.5690.0340.605
filter_mscore_freqobs0.1600.0030.164
filter_on_max_peptides0.1570.0050.162
filter_on_min_peptides0.1830.0080.190
filter_proteotypic_peptides0.1510.0040.155
import_data0.6150.0240.638
load_mart4.9920.1118.539
mscore4assayfdr0.5340.0410.577
mscore4pepfdr0.3660.0140.380
mscore4protfdr0.3230.0050.329
plot.fdr_cube0.2060.0060.214
plot.fdr_table0.2140.0080.223
plot_correlation_between_samples0.4720.0100.483
plot_variation0.5240.0050.530
plot_variation_vs_total0.4910.0050.497
reduce_OpenSWATH_output0.1690.0040.174
removeDecoyProteins0.1560.0030.160
sample_annotation0.1570.0050.162
transform_MSstats_OpenSWATH0.0030.0010.004
unifyProteinGroupLabels0.1400.0080.147
validate_columns0.0010.0010.002
write_matrix_peptides0.1700.0020.173
write_matrix_proteins0.1540.0020.156