Package: SWATH2stats

Version: 1.12.1

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_1.12.1.tar.gz

StartedAt: 2019-04-16 03:03:19 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:05:55 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 155.8 seconds

RetCode: 0

Status:  OK

CheckDir: SWATH2stats.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.12.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/SWATH2stats.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.12.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘imsbInfer’
* 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
Examples with CPU or elapsed time > 5s
                     user system elapsed
convert_protein_ids 0.519  0.043  13.409
* 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-3.8-bioc/meat/SWATH2stats.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SWATH2stats
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘SWATH2stats’ ...
** 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
* DONE (SWATH2stats)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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: 120 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 16.168   4.535  22.093 

name	user	system	elapsed
add_genesymbol	0.010	0.001	0.011
assess_decoy_rate	0.170	0.005	0.177
assess_fdr_byrun	0.244	0.012	0.258
assess_fdr_overall	0.228	0.008	0.241
convert4MSstats	0.797	0.026	0.831
convert4PECA	0.233	0.007	0.242
convert4aLFQ	0.909	0.026	0.939
convert4mapDIA	0.771	0.028	0.812
convert4pythonscript	0.171	0.002	0.176
convert_protein_ids	0.519	0.043	13.409
count_analytes	0.208	0.007	0.218
disaggregate	0.544	0.027	0.575
filter_all_peptides	0.226	0.010	0.237
filter_mscore_all	0.388	0.076	0.322
filter_mscore_fdr	0.996	0.488	0.698
filter_on_max_peptides	0.469	0.286	0.296
filter_on_min_peptides	0.917	1.226	0.302
filter_proteotypic_peptides	0.649	0.831	0.234
import_data	0.646	0.033	0.687
load_mart	0.440	0.014	3.901
mscore4assayfdr	0.392	0.020	0.413
mscore4pepfdr	0.382	0.018	0.401
mscore4protfdr	0.354	0.007	0.367
plot.fdr_cube	0.205	0.003	0.211
plot.fdr_table	0.218	0.005	0.226
plot_correlation_between_samples	0.750	0.014	0.769
plot_variation	0.617	0.028	0.648
plot_variation_vs_total	0.740	0.035	0.782
reduce_OpenSWATH_output	0.153	0.002	0.156
removeDecoyProteins	0.181	0.002	0.185
sample_annotation	0.162	0.002	0.165
transform_MSstats_OpenSWATH	0.006	0.001	0.006
unifyProteinGroupLabels	0.182	0.005	0.189
write_matrix_peptides	0.20	0.01	0.21
write_matrix_proteins	0.206	0.002	0.210