Multiple platform build/check report for BioC 3.11 - CHECK report for SWATH2stats on celaya2

##############################################################################
##############################################################################
###
### 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_1.17.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SWATH2stats.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.17.5’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'imsbInfer', '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 ... 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 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.

Installation output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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"
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 113 | SKIPPED: 0 | WARNINGS: 11 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 23.228   3.601  26.381

Example timings

name	user	system	elapsed
JPP_update	0.139	0.004	0.143
add_genesymbol	0.009	0.000	0.010
assess_decoy_rate	0.136	0.002	0.138
assess_fdr_byrun	0.601	0.020	0.623
assess_fdr_overall	0.304	0.020	0.325
convert4MSstats	0.644	0.045	0.689
convert4PECA	0.598	0.011	0.610
convert4aLFQ	0.683	0.042	0.726
convert4mapDIA	0.912	0.051	0.964
convert4pythonscript	0.270	0.003	0.273
convert_protein_ids	1.435	0.081	4.928
count_analytes	0.262	0.018	0.279
disaggregate	0.610	0.056	0.666
filter_all_peptides	0.236	0.013	0.251
filter_mscore_all	0.507	0.160	0.399
filter_mscore_fdr	1.179	0.382	0.972
filter_on_max_peptides	0.514	0.165	0.403
filter_on_min_peptides	0.855	0.519	0.349
filter_proteotypic_peptides	0.655	0.369	0.299
import_data	0.745	0.061	0.807
load_mart	0.421	0.023	3.965
mscore4assayfdr	0.727	0.110	0.838
mscore4pepfdr	0.610	0.057	0.667
mscore4protfdr	0.473	0.028	0.502
plot.fdr_cube	0.271	0.014	0.286
plot.fdr_table	0.333	0.018	0.353
plot_correlation_between_samples	0.676	0.016	0.693
plot_variation	1.086	0.079	1.166
plot_variation_vs_total	0.783	0.054	0.838
reduce_OpenSWATH_output	0.282	0.014	0.296
removeDecoyProteins	0.241	0.005	0.246
sample_annotation	0.170	0.003	0.173
transform_MSstats_OpenSWATH	0.009	0.001	0.011
unifyProteinGroupLabels	0.210	0.009	0.219
write_matrix_peptides	0.253	0.026	0.278
write_matrix_proteins	0.247	0.005	0.251

CHECK report for SWATH2stats on celaya2

Summary

Command output

Installation output

Tests output

Example timings